Compaore, who ruled the West African nation with a firm hand for nearly three decades, was forced to flee last October after an uprising when he attempted to change the constitution to enable him to seek a third term in office.
He has since sought exile in neighbouring Ivory Coast.
The National Transitional Council, which is acting as parliament, said its members had voted to indict the former president and members of his government.
Some of the ministers include former foreign affairs minister Djibril Bassole and former security minister Jerome Bougouma, who was also charged with embezzlement and illegal enrichment.
The ministers were not immediately available to comment.
“Former prime minister Luc Adolphe Tiao, who signed an order authorising the army to crush the October 30 and 31 uprising, was charged with assault and battery, murder and complicity to murder demonstrators,” the council said.
It said all other members of Compaore’s government who were present during a cabinet meeting on October 21, 2014, faced similar charges.
The transitional council is steering Burkina Faso back to constitutional rule, which will culminate with a presidential election in October.
The transition has been marred by tensions between the powerful Regiment of Presidential Security (RSP), Compaore’s well-armed praetorian guard, and the government led by Prime Minister Yacouba Isaac Zida, a former second-in-command of the elite unit.
The top court of the 15-nation Economic Community of West African states (ECOWAS) said on Monday that Burkina Faso’s move to exclude Compaore from contesting the October elections was illegal.