SECRETARY OF TRANSPORTATION Drew Lewis has successfully warded off a threatened strike mext month by the nation's airline pilots. But the price he has paid for this bit of labor peace is extremely high. He has undermined confidence in the Federal Aviation Administration and cast doubt on the validity of the answer the government must soon give to a major question of airline safety.

The Air Line Pilots Association has been threatening to strike if the government does not require three-man flight crews in the airliners of the future. It objected violently when the FAA last summer certified one of those planes as safe to fly with a two-man crew, and it was anticipating a similar decision on the certification of two more new airliners.

The compromise Secretary Lewis worked out was to turn the crew question over to a special presidential commission. He says pilots have agreed to abide by the commission's decision. The ALPA has withdrawn its strike threat.

The first trouble with this is that the secretary's action suggests he has doubts about the competence of the FAA to make a major decision that is clearly within the area of its principal responsibility -- aviation safety. This is compounded by his decision to reopen the certification the FAA granted to the DC9-Super 80 last summer. Does he think the FAA was wrong or inadequate? Or is it just a sop to the ALPA?

The other trouble is that by trying the resolution of a labor dispute to a safety question he has created a framework in which any answer the commission gives will be suspect. If it decides three crew members are necessary on these new planes, the inference will always exist that it acted as much on economic as on safety grounds.

The matter of aviation safety is far too serious to be treated so cavalierly. If Secretary Lewis has doubts about the quality of the FAA's performance, he should get them before the public promptly. If he doesn't he should have left this matter where it was and dealt with the ALPA on a basis that did not compromise a decision that is the government's, not a special commission's to make.