Maj. Gen. Charles Lyon said the service decided in 2005 not to make recommended changes that would have better regulated oxygen supplied to pilots. At the time, respiratory problems reported by pilots were not considered serious.
Since then, many more breathing problems have been reported, Lyon said, and the Air Force "has learned a lot" about physiological effects unique to the F-22.
Pilots have reported becoming disoriented while flying the plane.
"We're looking at making broader changes that would incorporate those  suggestions," Lyon said.
He was responding to a question by Rep. Jackie Speier, D-Calif., who asked specifically about a report in Thursday's Star-Telegram that the Air Force did not make changes that would have helped control the respiratory issues.
For years, pilots have flown the Raptor while breathing high levels of oxygen that collapse lung tissue.
The condition, known as acceleration atelectasis, results in coughing and respiratory difficulty that the Air Force has said was only a minor problem.
The general's comments came at a hearing of the Tactical Air and Land Forces subcommittee of the House Armed Services Committee on the Air Force's response to health and safety problems reported by F-22 pilots.
The Air Force is "certain the F-22 cockpit is a safe and effective workplace to operate," Lyon said. But preparations are far along to implement other modifications designed to make flying the F-22 safer and less stressful.
A modified pressure vest to combat the strain of G-forces should be ready by the end of the year. Lyon said that should aid breathing and reduce the chances that pilots will become disoriented.
The F-22, he acknowledged, is the only modern fighter without such a backup system.
In their testimony, Lyon and retired Gen. Gregory Martin, who headed an F-22 study by the Air Force Scientific Advisory Board, said more frequent operation of the Raptor since 2008 led to numerous physiological problems for pilots.
A comprehensive investigation was launched in 2011, but only after a fatal 2010 crash and several reports of pilots reporting
Part of the problem, Martin said, is the F-22 was developed during the 1990s after the Air Force had lost much of its scientific, medical and engineering expertise to
There is no evidence that F-22 pilots are breathing toxic substances, said Clinton Cragg, a NASA engineer advising the Air Force.
However, Cragg said, the F-22 oxygen system would not filter out many toxic substances that could cause respiratory or other problems.
Committee members mostly commended the Air Force. "On balance, I'm pleased with the level of effort the Air Force has put into this investigation," said Rep. Silvestre Reyes, D-El Paso.
But Speier said afterward that the Air Force "needs to recognize that it has a crisis on its hands, that its people can no longer trust that the leadership prioritizes [their] welfare. ... It is deeply troubling that they continue to underestimate the scope and the severity of the problem."