Major General Godefroid Niyombare, along with three other senior Army and police officers, was arrested on Friday after the coup to overthrow Burundian President Pierre Nkurunziza resulted in a failure. Niyombare is now afraid that the ruling government would "kill him".
Admitting that the coup had failed, Niyombare told AFP: "We have decided to surrender ... I hope they won't kill us."
His spokesman, Venon Ndabaneze, also confirmed that the troops loyal to Nkurunziza were arresting him, deputy coup leader Cyrille Ndayirukiye, and a few others.
A government spokesman told Reuters: "They will be held answerable."
Meanwhile, President Pierre Nkurunziza has returned to Burundi and is expected to address the nation from the country's capital.
The people were in support of the efforts to overthrow Nkurunziza, who has sparked widespread unrest after announcing his wish to run for a third term. However, they were met with heavy armed opposition from military loyal to the president.
On 13 May, Niyombare - who used to be a close ally of the Burundian President - announced via radio that the country no longer recognises Nkurunziza as their leader. Soon after the announcement, forces loyal to the coup leader closed down the Bujumbura Airport and the borders of the landlocked country.
The troops loyal to the president, however, were able to suppress the military rebellion by Thursday night.