The East African nation has been unearthing such graves from a past that includes massacres along ethnic lines. Some have warned that the work can be sensitive ahead of the presidential election in May.
The country's truth and reconciliation commission said the latest mass graves to be explored are in central Karusi province. There appear to be at least 18 such graves.
The province was plunged into crisis after the assassination in 1993 of Melchior Ndadaye, Burundi's first ethnic Hutu and democratically elected president. Some Burundians say ethnic Tutsi families were massacred after his death.
But the commission's president, Pierre Claver Ndayicariye, said the bodies were from 1972, when many ethnic Hutus were killed following a failed coup against leader Micombero Michel.
The people buried in the graves had been imprisoned and then taken in military trucks to the execution grounds, Ndayicariye said.
Some in Burundi have been critical of the commission's work and its choice of mass graves it chooses to investigate. Its mandate covers crimes committed between German colonization in 1885 to 2008 when the final rebel group signed a cease-fire agreement.
Emmanuel Nkurunziza, secretary of one Tutsi organization, called it "a shame to say thousands of thousands of dead bodies in Karusi are Hutus killed in 1972 while it is known that in 1993 Tutsis were exterminated in Karusi."
He added that "you cannot take Tutsis' bodies and call them Hutus."
In a statement on Monday, a coalition of political parties in exile said the commission should halt its work because it doesn't inspire confidence in all Burundians. The statement alleged that the commission was put in place to serve the interests of the ruling party.