Army chiefs had given Gen Gilbert Diendere a 10:00 GMT deadline to surrender or face an assault.
The army has ordered anti-coup protesters in the capital, Ouagadougou, to return home, amid fears of fighting.
Gen Diendere seized power last week with the backing of the presidential guard, but the army has remained loyal to the deposed government.
Its troops have entered the capital, vowing to retake it. The European Union (EU) has called on the presidential guard to immediately lay down their weapons to avoid bloodshed.
Army chief of staff Pingrenoma Zagre told France 24 news channel that he was in contact with Gen Diendere, and wanted to avoid conflict.
He added that he was awaiting “instructions” from the Economic Community of West African States (Ecowas) regional body, which had put together a peace plan for the former French colony.
Eleven regional leaders are holding emergency talks in Nigeria’s capital, Abuja, to discuss it.
At least 10 people have been killed and more than 100 injured since the coup in clashes between the presidential guard and protesters.
Gen Diendere staged the coup after opposing moves to integrate the presidential guard into the army.
Speaking at a press conference in the capital, he said he did not want bloodshed, but would defend himself if attacked.
Earlier, an army officer said talks with Gen Diendere had broken down.
“He wants a fight,” said the officer, who spoke to the BBC on condition of anonymity.
Gen Diendere says he will step aside once regional leaders endorse the peace plan at their summit.
He has released the interim president and the prime minister, following talks brokered by mediators.
France’s ambassador to Burkina Faso, Gilles Thibault, tweetedthat interim President Michel Kafando, who was arrested last Wednesday, was now at the ambassador’s residence.
In an interview with BBC Afrique, the general apologised to the nation for staging a coup, saying it was “the least we could do”.
“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’ decisions,” said Gen Diendere, who once served as chief of staff to Mr Compaore.
The presidential guard is loyal to Mr Compaore and installed Gen Diendere as the new leader last week – a month before elections had been due in the landlocked country.
Mr Compaore, who was in power for 27 years, was ousted in a popular uprising last year.
The interim president took office to pave the way for democratic elections.