ATLANTA, DEC. 5 -- FBI agents confiscated 13 homemade firebombs and "hundreds, maybe even thousands" of homemade machetes as they regained control of the federal penitentiary here today when the last of more than 1,100 rioting Cuban detainees surrendered, authorities said.

"The entire process went very smoothly and without incident," said Michael Caltabiano, executive assistant to the facility's warden.

The last detainee surrendered about 9 a.m., Caltabiano said, ending a process that had begun late Friday morning, about 11 hours after the inmates released unharmed the last 89 of 94 people held hostages since Nov. 23.

After the last surrender, 360 heavily armed FBI agents swept through the prison, finding some weapons but no booby traps, no one hiding and no bodies, authorities said.

In the 11-day uprising here, one inmate died, and several guards and inmates were wounded when Cuban detainees seized control and the hostages two days after Cuban inmates in Oakdale, La., did the same.

Both groups demanded that they not be deported under a revived diplomatic pactwith Cuba that provides for sending back about 2,500 Cubans who arrived in the 1980 Mariel boatlifts. A government agreement to review their cases ended hostilities here early Friday, six days after a similar pact in Oakdale.

In the agreement here, Attorney General Edwin Meese III agreed to a deportation moratorium of unspecified duration while administrators undertake case-by-case reviews of the detainees' eligibility for U.S. residency.

As inmates here filed out to surrender, they tossed homemade weapons -- including four-foot, double-edged machetes -- into a bin, Caltabiano said. Then they passed through a gate into the custody of waiting federal agents.

Weldon Kennedy, special agent in charge of the Atlanta FBI office, said the confiscated weapons included 13 homemade firebombs and "hundreds and maybe even thousands" of machetes. They were making them {in a prison workshop} from the very beginning, almost 24 hours a day."

The exiting prisoners were strip-searched and X-rayed for hidden weapons, Caltabiano said.

Most were then handcuffed and put on buses to be taken to nearby Dobbins Air Force Base for transfer to about a dozen other federal installations.

{More than 500 of the Cuban prisoners arrived today at Leavenworth (Kan.) federal penitentiary, bringing the number there to about 719 amid protests by Rep. James C. Slattery (D-Kan.) that the prison in his district has too few guards for them, the Associated Press reported.}

About 186 of the 1,104 Cuban inmates were being held today in a prison cellblock never controlled by the rioters, Caltabiano said. They may remain here because of overcrowding elsewhere, he said.

The rest of inmates who had not surrendered before the last hostages were released already have been transferred.

"They were all in reasonably good shape, obviously tired," said Gary McCune, regional director of the U.S. Bureau of Prisons. "There didn't appear to be any injuries from any conflict inside."

No injuries to the 89 hostages held throughout the siege have been reported.

Officials do not have an estimate of property damage to the prison, in which at least three buildings were burned as the inmates controlled about 80 percent of the federal facility.

In Washington, President Reagan today issued a written statement congratulating federal agencies involved in the crisis on its successful conclusion.