ATLANTA--Cuban inmates who took control of a federal penitentiary 12 days ago put down their weapons one by one yesterday and boarded buses for new cells elsewhere as their 89 hostages savored their first full day of freedom.

Despite an agreement reached late Thursday to end one of the longest prison standoffs in U.S. history, the 85-year-old prison remained in control of the detainees, some of whom were armed with machetes 4 feet long, authorities said.

It may be 24 hours before all the inmates have been removed, U.S. Justice Department spokesman Patrick Korten said.

"When the surrenders stop, we'll go in and take back the place by force if necessary," said Bureau of Prisons spokesman John Vanyur. "There is no indication that certain individuals have refused to come out--but it is a good possibility."

The first of the 1104 Cubans left the stone prison at noon after being strip-searched, X-rayed for weapons and handcuffed. They were taken to Dobbins Air Force Base, where they were placed on planes to one of 47 prisons nationwide.

Korten refused to specify the prisoners' destinations but said the Cubans would be spread out. Federal institutions are so crowded that some inmates will be paroled or sent to halfway houses to make room, he said.

Meanwhile, some of the freed hostages said they planned to catch up on sleep, go out to eat big meals and discuss the ordeal with their families.

"I feel very good, very relieved," said Carl Gates, chief psychologist at the prison.

"They treated me like a brother, a member of the family," said Gene Dixon, a freed legal technician.

Federal prisons here and in Louisiana were overrun late last month by Cuban inmates fearing deportation under a new immigration pact in which 2500 Cubans considered undesirable by the U.S. government would be returned to their homeland.

The eight-day siege at the detention center in Oakdale, La., ended Sunday when 1000 inmates released their 26 hostages.

The Atlanta uprising, which began November 23, ended early Friday when federal negotiators, inmate representatives and witnesses signed an eight-point agreement placing a moratorium on deportations of all Mariel detainees.

The pact applies to all 3800 veterans of the 1980 Mariel boatlift now, held in county, state and federal prisons nationwide, including those who took over the Oakdale center, said Korten.

"I don't think we yielded to the demands of hostage-takers," U.S. Attorney General Edwin Meese III said in Washington. "There are a lot of reasons why this agreement comports with fair treatment in this case. That will become clear when we can talk in detail about the agreement and the review process next week."

When the prison rioting began, there were nearly 1400 Cuban inmates and about 200 Americans locked up in Atlanta. By the time the takeover ended, 1104 Cuban and 17 American prisoners remained. The Americans are not covered by the pact.

At least three buildings were gutted by fires and one inmate was killed during the uprising.