"They said they were surrendering, but they continued to hide themselves so security forces captured them," Willy Nyamitwe, a media and communications adviser for Nkurunziza said, as quoted by the Wall Street Journal.
He did not specify the exact number of arrested.
Nyamitwe also stressed that Burundi's capital city Bujumbura is under government control.
On Wednesday, while Nkurunziza was in Tanzania for a regional summit, Maj. Gen. Godefroid Niyombare, who was fired as the chief of Burundi intelligence last February, announced the dismissal of the country's government.
On Wednesday and Thursday, Bujumbura saw violent clashes between forces loyal to Nkurunziza and the opposition, which at one point claimed to have seized most of the city.
Nkurunziza said on Thursday that the situation in the country was under control. Later that day, he said on Twitter that he had returned from Tanzania and thanked the people of Burundi for their patience.
Burundi saw weeks of violent protests over President Nkurunziza's decision to run for a third term in office, deemed unconstitutional by critics. Nkurunziza's supporters argue he has a right to take part in the upcoming elections, as for his first term he was appointed president by Parliament rather than standing before the electorate.
