The Metropolitan Washington Council of Governments called on American Airlines yesterday to suspend two controversial late-night flights into National Airport by DC9-80 jetliners and asked the Transportation Department to rewrite regulations that allow the flights.

The unanimous vote by COG, which links 18 state and local governments, came as Trans World Airlines disclosed it has become the second carrier to take advantage of the low-noise DC9-80's ability to meet the airport's noise limits for landings after 10 p.m.

Last Thursday, TWA moved back the scheduled arrival time of its chronically late Flight 240 from St. Louis by 26 minutes, scheduling it to arrive at 10:25 p.m., TWA spokesman David Venz said. The change was made to create a more realistic schedule, he said, and has generated no citizen complaints.

At yesterday's meeting of the COG board, Rockville Mayor John R. Freeland suggested that a boycott of American Airlines be organized if it continued its flights, which began on Aug. 31. "I don't think American Airlines could stand up to that, and I think we ought to test it," Freeland told the group.

COG also set up a special committee to coordinate political and legal actions designed to see that no passenger jet takes off or lands between 10 p.m. and 7 a.m. That, COG officials say, was the intent of a policy on noise and traffic put into effect at the federally owned airport in 1981.

Montgomery County Council member Scott Fosler called the beginning of the late flights "a giant step backward" for efforts to reduce traffic at National. "It was a shock," he said.

The board called on the Transportation Department to close the "loophole" that allows American to operate the flights. The department and the airlines argue there is no loophole. They say the policy set noise limits and any jet able to meet them is quiet enough to operate 24 hours a day.

Prop-powered commuter and private airplanes already operate through the night at National, they point out.

Spokesmen for American Airlines and TWA declined to comment on COG's actions.

The DC9-80, introduced in 1980, is still relatively rare in airlines' fleets. It is the only jet operating at National that meets the night noise limits for landing. It does not meet limits governing takeoffs. Republic Airlines has the planes but does not use them at National; Ozark Air Lines and New York Air have ordered them.

Under the current rules, jets that do not meet the night standards get a 30-minute "grace period" after 10 p.m. to land at National if they are running late. After that they must divert to another airport.

Venz said that before the Thursday schedule change, TWA's St. Louis flight sometimes reached the area after 10:30 p.m. but due to the DC9-80's low noise it was not required to go to another airport. "That flight has been getting in late more often than not for the past couple of months . . . and all that time no one has complained once to us," he said.

In another development, Alexandria has filed suit in federal court to stop the Federal Aviation Administration from testing new flight paths from National that are intended to distribute jet noise more evenly across the Washington area.

In a suit filed Tuesday at U.S. District Court in Alexandria, the city contended the FAA had failed to meet federal requirements for a full environmental impact study.

The test, which FAA officials say probably will begin in early October, was requested by COG. Alexandria has charged that it will intensify noise to which city residents are exposed. Fairfax and Arlington counties and the District also oppose the plan.