ATLANTA, DEC. 2 -- Negotiations to end the 10-day-old siege at the federal penitentiary here progressed slowly today, with the Cuban inmates demanding "clarifications" of the government's intentions and apparently grappling with one major "stumbling block."

Federal officials continued to express optimism that the takeover will be settled peacefully and the 89 remaining hostages released, but they cautioned publicly and privately that the standoff could last a while longer.

Cuban inmates, who have gathered by the dozen on the rooftop of the prison hospital to wave and shout to relatives and reporters, erected a tall, green Christmas tree decorated with white lights and red and silver garlands today, possibly as an indication that they are prepared for a long haul. It is unclear where they had found what appeared to be a fir tree and traditional trimmings.

A transcript of an audio tape from Auxiliary Bishop Agustin A. Roman of Miami was read in Spanish to the inmates today over the prison public address system. In it, Roman urged the inmates to "be very charitable with all the hostages" and not to "ask more than the law permits."

Roman told a Miami television station that he probably will come here Thursday and that he anticipates an end to the crisis by the time he arrives. Roman was instrumental in ending a similar takeover at the Federal Detention Center in Oakdale, La.

In Miami, Rafael A. Penalver, speaking for Roman, said the bishop has long supported judicial review of the cases of the Cuban detainees but that "under the circumstances" Roman thinks that the terms of the Oakdale agreement are adequate.

Cuban inmates in Oakdale released their 26 hostages Sunday, a day after Roman urged them in a videotape to sign the agreement they had reached last week with federal negotiators.

Officials said today that inmates in Oakdale had destroyed some immigration records during their nine-day uprising but that most of the documents can be duplicated.

Gary Leshaw, an attorney with the Coalition to Support Cuban Detainees who has been allowed to advise the six inmate negotiators, met privately with them for 90 minutes today and then with government negotiators.

Leshaw said the inmates asked numerous legal questions, but he refused to be specific, other than to say that one major issue is getting in the way.

"They trust me, and they wanted answers to certain things," said Leshaw, who gained access to the inmates as part of a deal to release a hostage Tuesday night. The inmates, speaking over loudspeakers, said the hostage's release also was a 29th birthday present for the coalition's coordinator, Carla Dudeck.

"I would say there's one kind of major issue that's kind of a stumbling block," Leshaw said today. If that can be settled, he said, "there would be a good chance we could resolve everything else."

Although Leshaw and federal officials refused to discuss details, the Cubans' chief concern has been that none of them is returned to Fidel Castro's Cuba. Most of them arrived during the 1980 Mariel boatlifts and lost their immigration parole after they were convicted of crimes in this country.

Some government sources said they fear that the "clarifications" demanded by the inmates may delay a settlement further because the government will not negotiate any agreement that allows all the detainees to remain in the United States.

The Oakdale agreement, they said, probably would not allow significant numbers of inmates to remain in the United States. A much greater number of inmates at the prison here are regarded as hard-core criminals, and it is unlikely that they would be given a better deal than the less dangerous Oakdale prisoners.

One government source said that Mexico, the country of asylum most often mentioned by inmate negotiators, might be a solution to the impasse over what happens to the detainees who are not accepted by the United States but do not want to return to Cuba.

"It sure sounds like a promising idea," the source said. However, he added, "We'd have to give them {the Mexicans} something in return."

Justice Department spokesman Patrick S. Korten said today that the government always has intended to apply any agreement reached here to the Oakdale prisoners, making any concessions here doubly important.

Korten said the government remains optimistic about an agreement will be reached, but he added that "there is no way at this point to determine when or whether settlement will be reached."

Korten also indicated that federal negotiators think that the divisions among the inmates are subsiding and that inmate negotiators are speaking for a majority. Korten said two more negotiators have joined the four who have been talking to FBI agents for several days.

And although Korten would not say directly that the two were part of the "radical" faction that has been blocking agreement, he said that inmates appear to be "fully represented."

Two more inmates left the prison today because they were ill, Korten said, bringing the total number of inmates holding the prison since the uprising began Nov. 23 to 1,107 Cubans and 18 Americans.