Security forces have meanwhile besieged his followers still barricaded in the building, according to negotiators and other officials.
"Also detained with Antauro Humala were some of his followers," Prime Minister Carlos Ferrero said on Tuesday.
Ferrero issued a demand to the rebels remaining in the police post to lay down their arms and release the hostages.
"If this does not happen, it is the obligation of the government to re-establish order and it will, with the combined force of the police and armed forces," he warned.
Humala - a former army major forced to retire - and about 90 of his followers were in custody after turning themselves in to national police chief Felix Murazzo in the town's municipal building, a spokeswoman for Interior Minister Javier Reategui said.
"There are 30 or 35 who are still in the police station. It appears they are angry and some of them have been
Peruvian Interior Ministry spokeswoman
"He came with the idea of surrendering himself but a group of his followers were not in agreement," the spokeswoman said.
"There are 30 or 35 who are still in the police station. It appears they are angry and some of them have been drinking liquor," she added.
The interior ministry spokeswoman said security forces launched an operation to recapture the police station at approximately 10pm (0300 GMT).
The government has declared a
30-day state of emergency
But they did not storm the building, she added, fearing the rebels would harm the 10 policemen held hostage since Saturday and five soldiers captured on Monday.
Humala "was trying to get his followers to surrender, but it appears things have gotten out of hand", she said.
Humala's offer to surrender came as a 6pm curfew imposed on the town went into effect.
The curfew is part of a government-declared, 30-day state of emergency in the region that resulted in the deployment of 1000 troops.
A reporter who had seen Humala enter the municipal building about four hours earlier was ordered by police to go into a nearby hotel with other journalists minutes before the operation began.
The crackle of automatic gun fire could be heard outside.
The three-day stand-off began on Saturday when Humala and a group of about 125 armed men seized the police station in the remote Andean town, about 440km southeast of the capital, Lima.
Five police officers were wounded and 10 more were taken hostage.
A day later, the authorities said the group ambushed a police vehicle, killing four officers and wounding several others.
Local media have also reported that at least one of the rebels who was badly injured later succumbed to his wounds.