The General Accounting Office said yesterday that the Federal Aviation Administration has spent millions of dollars to buy and fly its own airplanes for trips that, in many cases, could have been made on cheaper commercial flights.

The GAO also said that spouses of top-ranking FAA officials rode free on many FAA flights when there was no need for them to make the trip.

The report is a continuation of a GAO investigation into use of government-owned aircraft that peaked last year when the GAO said that FAA Administrator J. Lynn Helms took no commercial flights on business during his first eight months in office. Congress subsequently passed a law restricting Helms on most occasions to commercial flights.

The new GAO report said that many FAA flights, recorded as necessary for FAA pilots to remain current, were taken for transportation instead. In those cases, GAO said, commercial flights would have been cheaper.

An FAA spokesman said that Helms does and has taken commercial flights, but that most of his flying during the time of the report was necessary to check the air-traffic control system after President Reagan fired 11,400 striking controllers in August, 1981. Spouses were carried, Pinto said, only if an extra seat was available.

The Transportation Department said it is taking several actions to reduce the cost of operating FAA and Coast Guard aircraft. One FAA and one Coast Guard plane will be relocated from National Airport to field stations, and noncommercial flights for transportation only will be limited to those carrying the top two officials of DOT, the Coast Guard and the FAA.