Negotiations between army chiefs and the presidential guard have stalled, a senior military officer said.
Troops are moving through the capital, as the deadline to Gen. Gilbert Diendere to surrender passed.
Gilbert Diendere staged a coup last week after opposing moves to integrate the presidential guard into the army.
He has released the president and the prime minister, following talks brokered by mediators.
The coup has been widely condemned, with the African Union suspending Burkina Faso’s membership.
Gilbert Diendere says he will step aside once regional leaders, due to meet in Nigeria, endorse a peace plan, including an amnesty for coup plotters.
Burkina Faso’s PM Isaac Zida was captured by the presidential guard in last week’s coup.
France’s ambassador to Burkina Faso, Gilles Thibault, has also tweeted that interim President Michel Kafando, who was arrested on September 16, has been released from house arrest and is now at the ambassador’s residence.
Speaking from a secret location, Gen. Gilbert Diendere said: “Ready to surrender? We are not there yet… We wish to continue the discussions and we say to all that we are ready to implement Ecowas’ [West African regional group’s] decisions.”
He also apologized to the population, saying an apology was “the least we could do”.
The Ecowas plan should be discussed by West African heads of state in Nigeria on September 22.
The presidential guard is loyal to ousted President Blaise Compaore and installed Gen. Gilbert Diendere as the new leader last week.
Since then, at least 10 people have been killed and more than 100 injured in clashes.
Burkina Faso’s army ordered the presidential guard to disarm before it marched on the capital.
“We must now secure the surrender of the [coup leaders] without gunfire or bloodshed,” Col. Serge Alain Ouedraogo, of the Burkinabe police, told AFP.
Ecowas’ plan includes the return to civilian government, an amnesty for the soldiers behind the coup and elections by the end of November.
Gilbert Diendere, who was the chief of staff to Blaise Compaore, led the coup a month before elections had been due in Burkina Faso.
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