For five years, America's most expensive fighter jets have been poisoning their pilots and crew. On Tuesday, the Defense Secretary finally stepped in – restricting the flights of the F-22 Raptor, and ordering the Air Force to begin an "expedited installation" of an automatic backup oxygen system for the entire fleet of Raptors, Pentagon spokesman George Little tells reporters. But Panetta is allowing the stealthy dogfighter to keep flying – for now.

The new oxygen systems will undergo flight tests through November, with installation beginning in December and proceeding in January 2013 at a rate of 10 planes per month. Additionally, the Air Force will have to fly its Raptors near a "proximate landing location" to make sure that pilots can land quickly if their planes' oxygen systems begin to fail. And the Air Force will both work with the Navy and NASA to figure out the Raptor's mysterious engineering flaw – whose root cause the Pentagon still does not know – and must now give Panetta monthly reports on its progress.

"There's no margin for error here," Little's colleague, Navy Capt. John Kirby, said. "Safety is a zero-sum game."

But Panetta isn't grounding any of the planes in the Raptor fleet – a step the Air Force took twice last year after pilots reported disorientation and other symptoms of "hypoxia," a condition indicating a lack of oxygen. "The secretary believes that this is the prudent course right now," Kirby told Danger Room. Ongoing flights "allow us to continue to examine the aircraft closely and to try to figure out what happened. There's a troubleshooting process that's going on right now, so the aircraft being in operation assists in that process."

At least 12 pilots have reported symptoms of hypoxia since April 2008. More mysteriously, F-22 ground crews have also reported hypoxia-like symptoms. At least one pilot may have died in connection with the oxygen problems, though the Air Force attributes the death to pilot error. On Tuesday, Sen. Mark Warner claimed that seven more Raptor pilots had contacted his office, hypoxia-like symptoms. And while the Air Force doesn't yet know the source of the problem, some aviation experts think the problem isn't suffocation, but rather amounts of engine oil contaminating the F-22's air systems.

Both spokesmen denied that Panetta had lost confidence in the Air Force's handling of the F-22 inquiry. "The Secretary believes that the Air Force leadership shares his sense of urgency," Little said. Neither explained why Panetta was stepping in to the Air Force's investigation, aside from calling him "deeply concerned with pilot safety."

Earlier this month, however, two Raptor pilots came forward to discuss the plane's flaws on 60 Minutes. They said they spoke for a "vast, silent majority" of pilots apprehensive about flying a jet that could choke them. The pilots sought out protection from Rep. Adam Kinzinger of Illinois, a fellow Air Force pilot, but that hasn't appeared to stop the Air Force from issuing a letter of reprimand to one of them that could herald the end of his career.

The F-22 will continue to fly, for the time being, even as the search for the engineering flaw continues. Panetta's rules limiting how far pilots can fly the F-22 are flexible – pilots must show a "prudent amount of proximity to a landing strip," Kirby said – in order to make sure pilots can complete their assigned missions. Still, that's a pretty serious restriction on an aircraft with a range of more than 1,600 nautical miles. But Little said it will mean "long-duration airspace control flights in Alaska will be performed by other aircraft."

Nevertheless, a scheduled deployment of Raptors to an airbase the United States uses in the United Arab Emirates, near Iran, will continue as planned.

The Air Force wants the F-22, one of the most advanced warplanes ever designed, to be among the centerpieces of its future. Yet the jet has never fired a shot in anger, and the persistent oxygen problem raises questions about whether it will any time soon. It is also one of the most expensive planes the Air Force has ever purchased, costing between $137 million and $678 million per plane depending on how you count. But the Pentagon isn't backing away from a plane that chokes its pilots.

"We still value it," Kirby said. "We still need it. It is a very powerful arrow in the quiver."