The General Services Administration is constructing a $56 million federal office building in downtown Boston that has become a hot topic around the agency.

The building, which originally was to be named after retiring House Speaker Thomas P. O'Neill Jr. (D-Mass.), could end up with only two-thirds the number of federal employes it was built to house, according to some GSA officials.

William F. Sullivan, GSA's public buildings commissioner, and Peter A. Thomas, the regional administrator in Boston, said it is unrealistic to predict the occupancy rate until the building is finished in a year.

But William A. Clinkscales Jr., GSA's associate administrator for policy and management systems, and Raymond A. Fontaine, GSA's comptroller, already are taking potshots at the project, contending that the Public Buildings Service failed to do enough planning. Both say that PBS officials should have realized that the number of employes had decreased since plans were drawn up and adjusted the plans accordingly.

"It's pure interference from Clinkscales and his cub detectives," Thomas countered. "They're always meddling in other people's affairs." Still, to fill the space, Thomas plans to move additional agencies into the new building. But some of those new occupants, including his own 48,000-square-foot regional office, will be moving out of other federal buildings.

Fontaine contends that some agencies have balked at giving up space they are renting for an average $15 a square foot for space in the new building at $25 or $30 a square foot. Agencies have to pay GSA for the space they occupy in federal buildings.

"Can you blame them?" Fontaine said. "They have to budget for that extra money."

Sullivan, who has been at GSA only a month, said rather than waste time debating the merits of the project, he'd rather go to the White House "and get them to force agencies to move into the building, if that's what it takes. This building will be filled with federal employes."

He paused, then added, "If not, we'll out-lease some of the space to the private sector. It's a very desirable building."

Thomas said that some of the Reagan administration's management changes are making it more difficult for GSA to manage office space.

"I don't even know if some of the agencies that are now supposed to go in there are going to be around in a couple of years," he said. ON THE BLOCK . . .

GSA has received the approval of the General Accounting Office to use private auctioneers to sell surplus government vehicles. William B. Foote, director of GSA's Personal Property Disposal Division, said about 30,000 vehicles are sold annually and the agency believes that it would be less expensive to turn the job over to a firm willing to round up the cars and trucks, recondition them, and put them up for sale. So far, one auctioneer, Carroll's Sales Co. of Felton, Del., has been hired to sell vehicles in the mid-Atlantic region. The company will make up to $168 for each vehicle it sells.

SPEAKING BUDGETESE . . . Two years ago, GSA developed a corporate-style annual report that tried to put its revenues and sales figures in understandable, layman's language that was different from the Office of Management and Budget's figures.

But John J. Lordan, deputy associate director of OMB for financial management, now says that GSA's figures are a little imaginative. "There seems to be no reconciliation between the budget totals . . . and the totals shown in the GSA revenue and expense statement," Lordan said.

Fontaine said Lordan is nitpicking and using GSA as a scapegoat because OMB opposes an accounting system that GAO has been supporting.