Air traffic controllers are overworked and disgruntled with their management, and it would be "prudent" to limit the growth in air traffic before the system loses its "proper margin of safety," the General Accounting Office reported yesterday.

The GAO, the investigative arm of Congress, told the Transportation Department that the Federal Aviation Administration cannot provide new labor-saving equipment or qualified controllers rapidly enough to keep up with growing air traffic in the next few years.

Therefore, "the only options available today are to continue to stretch the controllers or to limit the air traffic they are responsible for. Limiting air traffic before conditions worsen seems to be the prudent choice," the GAO said.

The report confirmed results of several major studies over the last two years that described the air traffic system as stretched too thin and less able to handle traffic than before the Aug. 3, 1981, strike by the Professional Air Traffic Controllers Organization.

President Reagan ordered that the 12,000 striking controllers be fired. The system was rebuilt with supervisors, nonstrikers and recruits. Today, it operates with fewer, less experienced controllers, the GAO said.

The report did not say directly that safety is being compromised but said that 70 percent of controllers in a systemwide survey reported that they are handling more traffic than they should handle.

The report also gave prominence to a statement from its prime consultant, the Flight Safety Foundation, a respected international air safety organization headquartered in Arlington, that "the present ATC air traffic control system does not provide the same level of safety as before the strike."

Rep. Guy V. Molinari (D-N.Y.), whose district includes some of the nation's busiest air traffic centers, called the report "a serious indictment of the air traffic control system."

FAA Administrator Donald Engen acknowledged in a telephone interview that the system has problems but said progress is being made toward resolving them. Meanwhile, he said, the system is operating safely.

"Yes, we have too much overtime out there," he said. "Is it unsafe? No."

Asked if he agrees with the GAO conclusion that tighter controls must be placed on air traffic, he said, "No sir, I do not."

Daniel Henken, a spokesman for the Air Transport Association, which represents the airline industry, said the GAO report "essentially corroborates our analysis" that traffic growth will require significantly more controllers. He said the FAA has consistently underestimated air traffic growth over the last few years.

The GAO based its report largely on a survey of 4,500 radar-qualified controllers, 1,000 of their immediate supervisors and 74 traffic and terminal managers. The report said the survey received a 75 percent response and that about 2,000 respondents volunteered extra comments.

Among the major findings:

*The FAA has met its goal of about 12,500 controllers, compared with 16,200 before the strike, but has fewer controllers at the highest experience level -- 8,300 today compared with 13,200 in July 1981.

*Retirement of experienced controllers will be a greater problem than the FAA has estimated, because of controller disgust with management and fears of changes under way in the federal retirement system.

Eighty-four percent of controllers and 81 percent of supervisors eligible to retire in the next two years said they will do so.

*Air traffic is growing rapidly so "controller workload will likely continue to be a concern for some time." Sixty percent of controllers said they are working too long daily without a break. A substantial number of supervisors agreed. The FAA is heavily dependent on controller overtime -- 908,000 hours in fiscal 1985 compared with 377,000 hours in fiscal 1980.

*About 1,300 extra comments were volunteered about management, 92 percent of them negative.

"What we think this all adds up to is that FAA needs to more fully consider the effects the growing demand for air traffic services is having on the controller work force," the report said. "Controllers at many major facilities are being stretched too thin and over time, the situation could impair their ability to maintain the proper margin of safety."