BUENOS AIRES, Argentina (AP) _ The leader of a military uprising was placed under arrest and his followers turned over one of two bases they held for five days. Rebels said they would give up the other base today, news reports said.

Questions persisted about whether a secret deal was made with the rebels, who demanded an end to prosecution of officers charged with human rights abuses during eight years of military dictatorship that ended in 1983.

Defense Minister Horacio Juanarena was to brief the Senate on Wednesday on how the government ended the uprising, which Argentines considered a threat to their 5-year-old democracy.

President Raul Alfonsin has said no concessions were made to the rebels. In brief comments to reporters at Government House today, Alfonsin stressed the need to end the revolt ''avoiding bloodshed that could have involved hundreds of Argentines.''

Rebel spokesmen denied they surrendered and said they negotiated a cease- fire that allows them to return, unpunished, to their units. The army said today that the rebels ''are at their units in accordance with orders'' of the army chief, Lt. Gen. Jose Dante Caridi.

It did not elaborate.

The leader of the estimated 500 rebels, army Col. Mohamed Ali Seineldin, surrendered Sunday night to military authorities but returned to the rebel arsenal later to supervise the dismantling of defenses, including trenches and land mines, at the arsenal.

On Monday night, he turned over the arsenal at Villa Martelli on the outskirts of Buenos Aires.

There had been conflicting reports concerning the timing of Seineldin's surrender. Initial reports said he surrendered Sunday, but unconfirmed reports later said he turned himself in on Monday. Officials today said the actural surrender was Sunday.

The revolt began Thursday, when an elite coast guard unit mutinied and joined troops who rebelled Friday at the suburban Campo de Mayo base. Most of those rebels moved to Villa Martelli base Saturday.

Seineldin organized the dismantling of the defenses, including trenches and land mines, he and his comrades had set up at the arsenal.

The army, in its statement today, said Seineldin is under arrest at a unidentified Buenos Aires garrison and will be questioned by a military judge. No mention was made of a trial or punishment for him or his supporters.

More rebels were at a base at Mercedes, about 60 miles west of the capital. The government news agency Telam said rebels intended to turn over that base to the government today.

The insurrection began before dawn Thursday and was the third military uprising in 20 months and the rebels' demands, including for a change in the military hierarchy and better pay, were also behind the two previous revolts.

It was clear this time that the rebels had wide support throughout the army. Five bases openly supported the mutineers and units at several others refused to help the government.

On Sunday, three people were killed when civilians outside Villa Martelli began throwing rocks and bottles at the rebels, who fired back, police said. La Nacion newspaper said police believe many of the estimated 600 demonstrators were from the Montonero urban guerrilla group.

The government had claimed victory early Monday, saying the military rebellion was over. But the public was skeptical because Seineldin and many of the renegades remained at the Villa Martelli base.

In contrast to the current situation, soldiers who participated in an April 1987 uprising were arrested, held incommunicado and taken to military prison. Soon afterward, however, three-fourths of the army's top generals were removed and Alfonsin proposed legislation limiting prosecution for human rights offenses only to the highest-ranking officers.

From 1976 to 1983, the country's military rulers conducted a so-called ''dirty war'' against leftists in which an estimated 9,000 people disappeared.