Is the Air Force's F-22 fighter jet making pilots sick?

Military officers rarely speak out against their services, but in our lead story you'll hear from two elite pilots who question the safety of Air Force's most sophisticated, stealthy, and expensive fighter jet, the F-22 Raptor. Maj. Jeremy Gordon and Capt. Joshua Wilson have chosen to stop flying the F-22 because they say during some flights they and other pilots have experienced oxygen deprivation, disorientation, and worse. They are concerned about their safety in the air, as well as the long-term health consequences. The Air Force says it is doing all it can to investigate and solve the problem, and are keeping the jets in the air with careful supervision of the pilots.

The following script is from "The Raptor" which originally aired on May 6, 2012. Lesley Stahl is the correspondent. Karen Sughrue, producer.

The shiniest jewel in the Air Force is its F-22 Raptor, a sleek, stealth fighter jet that the Pentagon says can outgun and outmaneuver any combat plane anywhere in the world. But for all its prowess, the Raptor has yet to be used in combat. It was designed to go up against an enemy with a sophisticated air force, which means it sat on the sidelines during the wars in Iraq and Afghanistan, leaving its 200 pilots to fly mainly training missions.

But the Raptor - the most expensive fighter ever - has been plagued by a mysterious flaw that causes its pilots to become disoriented while at the controls from a lack of oxygen.

Tonight, you will hear from two of them who have come to believe the jet is endangering their lives and those of the people in communities they fly over.

They are so concerned they have taken the extraordinary step of risking their careers by appearing on 60 Minutes in uniform -- and without permission -- to blow the whistle on a plane they love to fly.

When you hear about the F-22, it's always in superlatives: the newest, fastest, stealthiest, highest-flying, most gravity-defying, enemy-killing combat machine in the sky.

Josh Wilson: It's invincible. It's the bottom line.

Its pilots are highly-trained, and competitively chosen, the elite jet jockeys of the Air Force.

Jeremy Gordon: I firmly believe in the aircraft.

Major Jeremy Gordon and Captain Josh Wilson are with the Virginia Air National Guard, based at Langley Air Force Base near Norfolk. They're two of only 200 pilots qualified to fly the F-22.

Josh Wilson: Its ability to go up into lethal force where we need it. It is absolutely unmatched.

Josh has been flying it for two years, Jeremy for six.

Lesley Stahl: What makes it unique when you're flying it?

Jeremy Gordon: The ability to know what's going on all the way around you all the time.

Josh Wilson: It is just a phenomenal, phenomenal machine.

Both flew combat missions in the Iraq War. Major Gordon was awarded the Air Force's highest honor for heroism: the Distinguished Flying Cross. In Air Force evaluations, he was called quote "a superstar...flawless." Captain Wilson was called: "a superb officer with intense warrior spirit."

Josh Wilson: It was, you know, kind of a surreal experience.

Josh says that during a routine F-22 training mission in February 2011, he suddenly realized he was losing control.

Josh Wilson: Several times during the flight, I had to really concentrate, immense concentration on just doing simple, simple tasks. Our training tells you if you suspect something's probably going on, go ahead and pull your emergency oxygen and come back home. When I did make that decision to pull the emergency oxygen ring, I couldn't find it. I couldn't remember, you know, what part of the aircraft it was in.

Lesley Stahl: So this emergency ring was exactly where it should've been?

Josh Wilson: Uh-huh.

Lesley Stahl: You just couldn't figure it out.

Josh Wilson: I couldn't figure out. I did not know where it was.

The Air Force says Josh's extreme disorientation resembled a condition called hypoxia or oxygen deprivation. In training, pilots in that state can have trouble even identifying a playing card.

Jeremy Gordon: The onset of this is insidious. Some pilots will go the entire mission, land, and not know anything went wrong. There was a publicly announced incident of a jet in Alaska hitting a tree and the pilot was not aware that he ran into a tree.

Lesley Stahl: He didn't know he hit a tree?

Jeremy Gordon: That's correct.

After Josh's incident, his symptoms were so severe, the Air Force sent him to a hyperbaric chamber.

Lesley Stahl: Hyperbaric, like the bends. This is the first time we've heard that pilots are going into hyperbaric chambers.

Josh Wilson: We've had several.

Even pilots who never had a physiological incident in the air had problems on the ground, in the days after they fly the plane.

Jeremy Gordon: Amongst F-22 pilots, there's a term called the "raptor cough," that is--

Lesley Stahl: The "raptor cough"?

Jeremy Gordon: In a room full of F-22 pilots, the vast majority will be coughing a lot of the times. Other things-- laying down for bed at night after flying and getting just the spinning room feeling, dizziness, tumbling, vertigo kind of stuff.

Lesley Stahl: I had heard that other pilots, because of their fears of crashing from their own vertigo, whatever, that they're taking out additional life insurance policies.

Josh Wilson: They are. Absolutely. We are waiting for something to happen. And if it happens, nobody's going to be surprised. I think it's a matter of time.

After a rash of similar hypoxia incidents, the Air Force took the radical step of grounding the entire F-22 fleet in May of 2011. The Pentagon revealed there had been 14 of these events in the previous three years, a rate described by its own scientific advisory board as "unusually high...and unacceptable."

Josh Wilson: We've got two theories with the jet right now. On the one hand, we're not getting the quality or the quantity of oxygen that we need. On the other hand, they're thinking contaminants. Somehow we're not getting what we need, or we're getting poisoned.

The Air Force launched an investigation that focused on the plane's onboard oxygen-generating system, or "OBOGS", which takes air from outside the jet, passes it through the engine and through a chemical process to produce a concentrated oxygen that the pilots breathe.

But with the investigation still underway, the Air Force put the plane back in the air last September, even though, as Chief of Staff General Norton Schwartz told Congress, they still didn't know what was wrong.

[Norton Schwartz: We have been unable to identify a single engineering fault...]

Lesley Stahl: They didn't find the problem. They didn't find the cause, they didn't fix it and they sent the plane back up.

Josh Wilson: And we were eager to go. We couldn't wait to get back in the air.

Lesley Stahl: Well, wait a minute. They didn't find the problem?

Josh Wilson: No, they didn't.

Lesley Stahl: Why were you eager to go?

Josh Wilson: 'Cause we're pilots.

The Air Force justified the decision by giving pilots two new items to wear while flying, which were put on display at a recent news briefing.

Charles Lyon: This is a pulse oximeter.

Major General Charles Lyon is director of operations at the Air Force Air Combat Command.

Charles Lyon: The pilots fly with these. They're right on their arm. They look at them, and they check them. And if there's any indication of an abnormal oxygen rate, we terminate the flight.

The second was a charcoal filter designed to block contaminants the pilots might be breathing, and collect them for analysis. But less than a month after the planes began to fly again, another pilot suffered hypoxia.

Lesley Stahl: This was you. You had the first incident, right? In October?

Jeremy Gordon: Yeah, it was actually me and my wingman both had incidents on the same sortie.

Jeremy's jet was torn apart and analyzed, but there was no smoking gun. Pilots were told to keep flying so the Air Force could gather more data.

Lesley Stahl: Here's an email that we have seen from one of your fellow pilots. "I feel I'm in the most expensive group of lab monkeys ever assembled."

Jeremy Gordon: I haven't seen that one.

Josh Wilson: We have been--

Lesley Stahl: You feel like a lab monkey?

Josh Wilson: We have been told that we are data collectors. Our job right now is to go out and collect data.

After Jeremy's, the incidents seemed to escalate in number, or pilots reported more often. The count is now 11 in the seven months since the grounding ended.

Lesley Stahl: Does that sound like a lot to you or not?

Jeremy Gordon: It's an astronomical occurrence rate. This is totally just me in ball park, but probably unprecedented in flying, that many physiological incidents in that amount of time of the same type and same aircraft.

The Air Force has confirmed that they have never seen such high rates of hypoxia in any other aircraft, with 36 of the 200 pilots reporting an incident, or 18 percent.

On Monday, the Air Force invited us to an F-22 media event at Langley Air Force Base and admitted that even after calling in NASA and the Navy's deep divers unit to help, the root cause of the pilots' hypoxia remains a mystery. General Michael Hostage is head of the Air Combat Command which runs the F-22 program.

Lesley Stahl: Is there any consideration now in the Air Force to ground the plane again, to find out what's going wrong?

Michael Hostage: At this point, no. I don't see a reason to stand the plane down.

Lesley Stahl: But general, the cases still come. Do you have a feeling that the pilots are getting concerned?

Michael Hostage: I know they're concerned.

Lesley Stahl: And yet you're gonna keep flying them?

Michael Hostage: Yes ma'am. Ideally I want the risk as low as possible. I'm not able to drive it as low in this airplane as I am with others because of this unknown circumstance, but I have driven it down to a level where we believe we can safely operate the airplane.

Lesley Stahl: Why is it taking so long to find out what the problem is?

Michael Hostage: Well, if I knew what the problem was, it would be gone. I just have not found the problem yet.

Lesley Stahl: In your opinion, is the F-22 safe to fly?

Jeremy Gordon: I'm not comfortable answering that question directly. I am not comfortable flying in the F-22 right now.

Josh Wilson: I am currently not flying the aircraft.

In a rare show of defiance for Air Force officers, both men informed their command in January they were going to stop flying.

Lesley Stahl: The Air Force says there is an inherent risk in flying. Period. Any of these planes.

Josh Wilson: Yes.

Lesley Stahl: Kind of sounds like, "Man up, guys. There's a risk. Come on."

Jeremy Gordon: Absolutely there's an inherent level of risk, just like there's an inherent level of risk of driving.

Lesley Stahl: You mean if there's a mechanical risk?

Jeremy Gordon: There's a mechanical risk or even an enemy threat where I'm trained to deal with that threat. But this is something strapped to my face under which I have no control what's coming through that tube which means there may be a point when I don't have control over myself when I'm flying.

To make matters worse, some of the pilots began coughing up black sputum. Air Force doctors cut into oxygen hoses, found - as this doctor's photo shows - black residue. And determined that the new filters that were supposed to be protecting pilots were shedding charcoal and pilots were breathing it in.

Lesley Stahl: Have the doctors spoken out? Have the doctors come forward and said, "Our pilots are having serious issues here. We have to find the cause and until we do these pilots shouldn't be up there"?

Josh Wilson: Absolutely.

Jeremy Gordon: Yes.

Lesley Stahl: They have?

Josh Wilson: Absolutely.

Well, just last week the Air Force quietly removed the filters. They plan to install a new filter - date undetermined. So where does all this leave our two pilots?

Two weeks after Jeremy stopped flying, he was called in.

Jeremy Gordon: I was asked to make a decision that day whether I wanted to fly or find another line of work.

Lesley Stahl: Fly or you're out?

Jeremy Gordon: That was it.

At that point, Jeremy's Air Force doctor put him on "do not fly" status for medical reasons. In Josh's case, he's been reprimanded for not flying. His salary cut substantially, and summoned to a hearing next week.

The pilots could face further disciplinary action for speaking to us which is why this man was seated just off to the side throughout the interview. He's Congressman Adam Kinzinger of Illinois, an Air Force pilot himself, who Josh and Jeremy went to with their concerns in order to gain protection under the Military Whistleblowers Act.

Lesley Stahl: So Congress passed a law for just this situation?

Adam Kinzinger: Yeah. Congress granted protection to whistleblowers in general and specifically military to say: if you have a concern, you know - not something obviously little - but something pretty big and serious, you have--

Lesley Stahl: Like this--

Adam Kinzinger: Like this -- you have a right to talk to your congressman because just 'cause you join the military doesn't mean you give up your right to citizenship.

Kinzinger thinks the Air Force is wrong to punish any pilot who doesn't want to fly for health reasons. And Josh and Jeremy are not the only Raptor pilots choosing to "stand down."

Josh Wilson: There have been squadrons that have stood down over concerns. And there's been threat of reprisals. There's been threat of flying evaluation boards clipping our wings and doing ground jobs. And, you know, in my case potentially getting booted out of the Air Force. So right now there's an example being set of, "Hey, if you speak up about safety, you're gonna be out of the organization."

For the Air Force, grounding the Raptor again would be an embarrassment. Originally the plane was touted as being more trouble-free than older fighters.

Lesley Stahl: Do you both want to see the Air Force ground this plane right now?

Jeremy Gordon: I want to see the jet fixed. Like a root cause identified--

Lesley Stahl: But do they have to ground it to find that out?

Jeremy Gordon: I don't know. I really don't know.

Lesley Stahl: Do you think they should ground the plane?

Josh Wilson: I think we grounded it for a reason, you know, back a year ago. We haven't done a single thing to fix it. So I think we need to reassess why we got back in the air in the first place.

Lesley Stahl: Do you think that a majority of the pilots would agree with you?

Jeremy Gordon: I think a vast majority, even--

Lesley Stahl: A vast majority?

Jeremy Gordon: --even though it's a silent majority.