The Senate Appropriations Committee voted yesterday to put the 800-bed D.C. prison construction project on hold while three alternative sites are reexamined -- a move that city officials say will cost them millions of dollars in delays and will further complicate the city's prison crowding problem.

As part of the site preparations for the prison, the city had demolished four large buildings and several smaller facilities in the area, and had relocated police and community mental health and alcohol abuse programs.

Sen. Tom Harkin (D-Iowa), chairman of the D.C. appropriations subcommittee, said he sought the delay after receiving numerous complaints from residents near the site of the proposed $50 million prison, adjacent to the D.C. Jail in Southeast Washington.

Harkin -- who succeeded Sen. Arlen Specter (R-Pa.), a major booster of the current prison project, as chairman of the subcommittee in January -- also said that recent significant "archeological findings" on the 10.5-acre site necessitated shifting the prison elsewhere.

"It's my opinion there are more suitable sites that would not disrupt neighborhoods and that would be more economic," Harkin said. "By finding a new site {without artifacts}, we may actually expedite construction."

The committee's action surprised city officials because it constitutes a 180-degree turnaround from previous action in which the committee ordered the city to sign a construction contract for the project by Oct. 15, 1986, and specified that the federally funded facility would be located near the D.C. Jail.

In approving the District's $3 billion fiscal 1988 budget, the committee voted to delay the project until at least Feb. 1, when the General Accounting Office and the Federal Bureau of Prisons will issue recommendations on whether the prison should be moved to one of three other sites: A 15-acre L-shaped tract adjoining the historic New York Avenue Brickyard in Northeast Washington. The property is part of the National Arboretum operated by the U.S. Department of Agriculture.

The 16-acre Anacostia Park/Fort Lincoln site, located along the Anacostia River, south of the Penn Central Railroad line. The tract is jointly owned by the National Park Service and the Department of Housing and Urban Development.

A 21-acre South Capitol Street site, on the south side of the Frederick Douglass Bridge, near Bolling Air Force Base. The District owns about five acres of the site and the federal government owns the rest.

City Administrator Thomas M. Downs termed the committee action "troublesome" and warned that if Congress goes along with the plan, it might cost the city $5 million to $10 million in contract penalties and wasted site preparation costs. Moreover, the three alternative sites already have been ruled out by federal officials, according to Downs. "I don't know what we'll do now," he said.

Specter, the prime force behind the prison project, began pressuring Mayor Marion Barry to go along with the idea in late 1984 as a means of complying with a series of court orders to relieve crowding at Lorton Reformatory and the D.C. Jail.

Specter, a former Philadelphia prosecutor, pushed through the first $30 million in federal funding for the prison in 1985 after Barry reluctantly endorsed the idea. Last October, Barry announced that a joint venture of Gilbane Construction and Sherman R. Smoot companies had been awarded the $49.8 million contract to build a five-story medium-security prison and drug treatment center, to house 700 to 800 inmates. Under the contract, the city must pay the joint venture $8,800 per day in penalties for any delays in the project.

A scheduled June groundbreaking was put off until the fall, according to city officials.

This month, Engineering Science Inc. of Washington, under contract to the city, reported discovering archeological deposits on a portion of the prison site.

Flossie Lee, chairwoman of the Advisory Neighborhood Commission 6B and a leader of a 500-member task force of residents near the present prison site, hailed the committee's postponement of the project. The group argued that its neighborhood already was troubled by congestion, pollution and hazards generated by the D.C. Jail, D.C. General Hospital, the D.C. Armory and Robert F. Kennedy Stadium.

The Appropriations Committee also:

Approved an amendment introduced by Sen. Don Nickles (R-Okla.) requiring full disclosure and audit of expenditures from the mayor's ceremonial fund. The fund's records were kept secret until recently. Approved report language instructing the D.C. Fire Department to take immediate steps to ensure that two qualified divers and scuba equipment are acquired by Jan. 1 for each of the four rescue squads and two fireboats. Urged the city to consider changing its residency requirement for city workers, which police and firefighter union officials contend works a hardship on their members. Staff writer Sari Horwitz contributed to this report.