The Federal Aviation Administration is ready to cut commercial air traffic at 41 airports by thousands of flights a day if mandatory budget cutbacks take effect Oct. 1.

Air security and aircraft maintenance inspections also would be trimmed, the agency said.Under the terms of the Gramm-Rudman deficit reduction act, the budget cuts will occur automatically unless White House and congressional negotiators reach a compromise agreement before Oct. 1, the start of the 1991 fiscal year.

A spokesman for the airline industry said the reductions would prove "terribly disruptive."

The aim of an emergency contingency plan issued Wednesday is to keep the number of daily flights at a level that the FAA's reduced force of air-traffic controllers could safely handle.

The FAA said the 40,000 flights that are normally handled by the 41 airports on an average day would be cut by 6,000. It said cancellations and delays could rise dramatically during bad weather. The Salt Lake City airport was among those mentioned.

Smaller airports also are likely to be affected when flights to and from the larger airports are canceled, the FAA said.

"The Gramm-Rudman reductions would cut deeply into the muscle of the Federal Aviation Administration, as well as other government agencies," said FAA administrator James B. Busey.

Robert J. Aaronson, president of the Air Transport Association, which represents the nation's major air carriers, said the plan will force "drastic cuts."

"The proposed reduction will be terribly disruptive to the nation's air-transport system, its passengers and shippers," Aaronson said, contending the situation illustrates that FAA's air-control functions cannot be operated efficiently "as long as the agency is the captive of the federal civil service and budget systems."

But he said the possibility that cutbacks will take effect is real and that airlines have already begun planning to deal with it.

The FAA said that if the budget cuts take hold it would have to furlough each of its 17,200 controllers for two days every two weeks, an overall manpower reduction of 25 percent on any given day.

The FAA calculated the maximum amount of traffic the reduced force of air controllers could handle safely at each of the 41 airports.