"As a sign of easing tensions and in the general interest, the national council for democracy has decided on the release of ministers and Michel Kafando," said a statement, adding that Kafando had been released late on Thursday.
There were no specific details about Prime Minister Isaac Zida, AFP reported.
Soldiers from the elite presidential guard burst into a cabinet meeting Thursday and seized Kafando and the others.
The coup -- led by General Gilbert Diendere, close to ousted strongman Blaise Compaore -- triggered street protests outside the presidential palace.
Three people died from gunshot wounds and at least 60 others were treated for various injuries, doctors at the main hospital in Ouagadougou, the capital, said.
The unrest hit the landlocked west African nation just ahead of presidential and legislative elections scheduled for October 11 -- the country's first since veteran leader Compaore was forced out last year.
Diendre, speaking to AFP hours after seizing power, said he still wanted elections to take place.
"Our wish is to reorganize ourselves and to move towards elections soon," General Gilbert Diendere said, while refusing to give a date for a vote.
"But we plan to discuss all that with the concerned actors, notably the political parties and civil society organizations to establish a timetable that allows us to move towards presidential and parliamentary elections."