The other six dead were soldiers, the west African country’s government said at the weekend.
It happened when government troops took on rioting mutineers for the first time, at their military base in second city and commercial centre, Bobo Dioulasso.
This came after several days of angry protests by soldiers who have been demanding better pay. The soldiers had also started looting the city and letting off gunfire. They began protesting nationwide in February, after which President Blaise Compaore promised them a range of benefits, and sacked his security chiefs in April.
The turmoil was also combined with demonstrations by trade unions and civil society groups angry at the rising cost of living and it is being viewed as the biggest challenge to Mr Compaore's rule since he seized power in a coup 24 years ago.
On Friday the President sent in a unit of his presidential guard, backed by parachute commandos and police in the first military intervention since unrest broke out.
Six soldiers in the army camp who fought back were killed during the operation in south western Bobo Dioulasso and a young girl was killed in the crossfire, security minister Jerome Bougouma told the media on Saturday. He said 25 ordinary people and eight soldiers were also hurt but the uprising was stopped.
The troops "have put an end to the schemes of the mutinous soldiers," Bougouma told Agence France Presse.
"We have arrested more than 57 mutineers," he said. "A search operation is continuing with the help of the public to arrest those on the run."
"The government remains ready to negotiate, to talk," but in the case of new "excesses," order and discipline will be restored, he said.
About 57 soldiers may now face trial, Justice Minister Jerome Traore said. "We are currently collecting weapons, ammunition and stolen items,” said a commando involved in the operation. “This could take one to two weeks, because lots of things were taken."
People living in Bobo Dioulasso said the city was calm by Friday night but the presidential guard stayed in the city. Bobo Dioulasso’s mayor, Salia Sanou, said part of the market had been ransacked by the mutineers.
France, which used to rule the country, said it was keeping a close watch on the situation in the country where many French nationals live. It said that the government should start talks with everyone involved to clear the way for reforms and bring back order.
Burkina Faso is rated by the United Nations as the world's third poorest country. It has faced internal and external worry over the state of its economy and human rights, and allegations that it was involved in the smuggling of diamonds by rebels in Sierra Leone.