The federal government's planning overseer approved a proposal here yesterday that in the next 40 years may turn a deteriorating 60-acre site in Southeast Washington into a massive office complex for up to 30,000 federal workers.

The long-range plan, approved unanimously by the National Capital Planning Commission, calls for constructing more than 6 million square feet of office space, an amount that is nearly twice the size of the Pentagon.

But change is not likely to come soon at the 16-block site, now filled with a hodgepodge of old and unsightly warehouses, former munitions manufacturing plants, parking lots, government offices and vacant buildings. The tract is bounded on the north by M Street SE, on the south by the Anacostia River, on the east by Isaac Hull Avenue and on the west by First Street SE.

Jack Binford, a General Services Administration official and a member of the commission, said that starting in July the agency will make some road improvements at the site costing more than $1 million. But he said GSA had no money allocated beyond that for construction of any new buildings.

He said that even if construction money is available as soon as 1987 the first building would not be completed until 1991, about a year after Metro's Navy Yard subway station is scheduled to open at M Street and New Jersey Avenue toward the northwest corner of the site.

The plan is the fourth for the area in the last 20 years, with the others falling victim to government inertia, lack of funding, and changing views about what should be done with the site.

A 1968 plan called for offices for 20,000 workers. But the newest plan calls for less space for up to 30,000 workers, in part because of the eventual availability of Metro service to the area and the fact that the government has decided in the last few years that federal workers need less, not more space in which to do their work.

With construction of new offices at the site still a long-range proposition, no federal agencies have been designated to move to the so-called Southeast Federal Center. Binford said agencies most likely to go would be those now housed in more costly rental space and those whose offices are scattered throughout the area.

The Navy has eyed the site for years, proposing to move 18,000 workers to the area, including the adjacent Navy Yard, primarily by moving employes who work in leased space in Crystal City. But the Navy plan has drawn the wrath of Virginia politicians, particularly Republican Sen. John W. Warner, who say it would adversely effect Arlington County's economy.

The National Oceanic and Atmospheric Administration, with offices in various locations, also has coveted the Southeast site for a central office, Binford said.

The Southeast Federal Center would be densely developed, Binford said, but it would not be "a megastructure like the Pentagon."

He said the buildings would be no more than 12 or 13 stories, similar to office buildings on K Street NW.

Jerry Shiplett, GSA's regional facility planning chief, said the development will "attempt to open the area back up to the fabric of the community. It's an effort to get away from the extraordinarily large federal buildings . . . like those on the Federal Enclave" downtown.

Nonetheless, one commission member, John G. Parsons, a National Park Service official, objected to the size of the development and its lack of parks and plazas.

"It's so dense . . . it's not a good environment for workers," Parsons said.

At his suggestion, the commission deleted a proposed boulevard along the Anacostia River and replaced it with a park.