A security source said at least 22 people were killed in the jihadists' assaults on the Burkinabe capital's four-star Splendid hotel and the nearby Capuccino restaurant, which are popular with UN staff and foreigners.
Thirty-three of the 126 people freed from the Splendid hotel by Burkinabe troops backed by French special forces were wounded.
"The attacks on the Splendid Hotel and the Cappuccino are over. But an assault is ongoing at the Hotel Ybi" next to the Cappuccino, Interior Minister Simon Compaore told AFP.
Twenty people have been confirmed dead, but the toll could rise further as Compaore told AFP earlier in the night that firefighters had seen 10 bodies on the terrace of the restaurant.
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"We don't yet have a total tally of the dead. The Burkinabe forces are still combing the hotel," he said.
Communication minister Remis Dandjinou told AFP the assault was carried out by Burkinabe troops with the support of French special forces. He also said that among those who escaped unharmed was Labour Minister Clement Sawadogo.
"It was horrible, people were sleeping and there was blood everywhere. They were firing at people at close range," Yannick Sawadogo, one of those who escaped, told AFP.
"We heard them speaking and they were walking around people and firing at people who were not dead. And when they came out they started a fire."
The attack comes less than two months after a jihadist hostage siege at the luxury Radisson Blu hotel in the Malian capital Bamako left 20 people dead, including 14 foreigners -- an attack claimed by the same Al-Qaeda affiliate behind the unfolding Ouagadougou assault.
He quoted one of the wounded as saying there were "more white people than black" among the dead.
Al-Qaeda in the Islamic Maghreb (AQIM) claimed responsibility for the attack saying it was "revenge against France and the disbelieving West", according to a statement carried by US-based monitoring group SITE.
The attackers were members of the Al-Murabitoun group based in Mali and run by Mokhtar Belmokhtar, SITE said.