Federal Aviation Administrator J. Lynn Helms strongly defended his air-traffic control system yesterday against suggestions that it is being restored too swiftly and perhaps at the cost of safety as it recovers from the 1981 controllers' strike.

In testimony before the House Public Works and Transportation subcommittee on investigations and oversight, Helms attacked a recent National Transportation Safety Board report questioning the system's safety.

The report "is simply not a high-quality document" and the board's findings suffered "from a lack of scientific control over the methodology used," he said.

NTSB Chairman Jim Burnett, in his testimony, agreed that the board's study is subjective in nature. Nonetheless, he reiterated his central problem, the one with which Helms apparently has the most difficulty:

"I am concerned that priority has been given to allowing air traffic to rise" when the FAA could have concentrated on returning air-traffic supervisors to supervising and on decreasing a controller's workweek.

Since President Reagan fired 11,400 striking controllers in August, 1981, supervisors and controllers who did not strike have kept the system in operation while training newly hired replacements.

Strict restrictions imposed on the number of flights have been steadily eased so that by the end of this year the system could handle as many airplanes daily as before the strike, Helms has said.

Helms told the subcommittee that, despite NTSB concern, he has reduced the number of flights that air-traffic facilities have told him they could handle and has retained enough capacity to cope with contingencies, such as an enormous snowstorm.

Subcommittee Chairman Elliott H. Levitas (D-Ga.) and other members asked Burnett several times if the system is safe. Each time, Burnett hedged, saying once, "I'm not Duncan Hines. The safety board does not like to give seals of approval."

Levitas asked Helms if he has been receiving substantial pressure from airlines and other aviators to eliminate flight restrictions. "I'm not pressurable," Helms said.

However, when Levitas later asked Helms to detail, airport by airport, how much capacity he has withheld, Helms said, "Is there a way we can do this without putting it in the record?" Every time something such as that is made public, he said, someone in the aviation community asks to use such capacity.