The General Services Administration has paid more than $500,000 for office space in New York City that has been vacant since GSA leased it nearly two years ago, according to a draft of an internal GSA audit report.

The report says GSA was supposed to pay $228,000 to have the offices at 1 Lefrak City Plaza in Queens altered for occupancy by federal agencies. But GSA delayed making the alterations, and it appears the space will remain vacant for the remaining year of the lease, the report says.

The total loss to taxpayers would then be about $800,000, the report says.

Rowland G. Freeman III, who became GSA administrator last summer, said yesterday the New York regional office has not yet given him a response to the audit report. "I haven't any answers for you," he said.

Richard Q. Vawter, GSA's public information director, said the lease was awarded when then-GSA administrator Jay Solomon was changing GSA's procedures for altering rented space.

As a result, he said, "GSA people got behind on it. It's a quirk," he said.

Meanwhile, a controversy over Freeman's demotion of William A. Clinkscales Jr. as director of GSA investigations continued to build yesterday.Clinkscales, who is credited by prosecutors with helping to start the GSA corruption investigations by referring cases to them, was named a deputy last week, overseeing nine GSA employes.

Clinkscales charged in a letter to the federal Merit System Protection Board that the transfer from a post where he had supervised 150 employes is "illegal, improper, and (constitutes) reprisal and political harassment."

Clinscales said that the Senate Governmental Affairs subcommittee on federl spending practices, headed by Sen. Lawton Chiles (D-Fla.), plans to hold hearings later this month on his transfer.

If he accepted the transfer, Clinkscales wrote, ". . . I would be unable to assure that critical evidence (for the hearing) is safeguarded."

Clinkscales' transfer was requested by his new boss, GSA Inspector General Kurt Mullenberg, who said he had been unable to develop a "professional relationship" with the 52-year-old investigator. Mullenberg has been criticized by Chiles for failing to develop any significant corruption cases while at GSA.

So far, 80 persons have been indicted in the GSA scandal. More indictments are expected this week.

Freeman and Mullenberg have sought to minimize the extent of corruption at the federal housekeeping agency.

The audit report said GSA subleased the office space in Queens from Stone and Webster Engineering Corp., which itself had subleased the space.

Although GSA knew at the time that alterations were needed and that the space had been vacant for several years, the agency leased the space immediately, the report said.

The auditors called GSA's subsequent efforts to alter the space "languid."

"In view of the fact that the sublease does not have a renewal option," the auditors said, "we question the wisdom of proceeding with space alterations until a renewal option is obtained."

The audit was prepared under the direction of Howard R. Davia, GSA's chief of audits, who has expressed concern that his job, like Clinkscales', may be in jeopardy.

In a letter to his senator, Harry F. Byrd Jr. (Ind.-Va.), Davia, whose audits have exposed major areas of abuse at GSA, said, "At the present, I sense a significant career peril in pursuing investigative audits that I have currently under way."

Davia is also expected to testify before Chiles' subcommittee.

Asked about Clinkscales' demotion yesterday, Freeman said, "What controversy? I don't anticipate that anything I do at GSA will be without difficulty."