On Thursday, the government accused the M23 militia -- with whom it is locked in a months-long conflict -- of slaughtering 50 people at Kishishe, a village around 70 kilometres (40 miles) north of the city of Goma.
The M23 hit back, saying the allegations were "baseless" and denying that it targeted civilians.
At a council of ministers meeting on Friday, the DRC's president Felix Tshisekedi "condemned in the strongest terms the massacre of more than 100 compatriots in Kishishe", government spokesman Patrick Muyaya said.
He said Tshisekedi had "instructed the government to declare three days of national mourning," adding that flags would be flown at half-mast throughout the country.
The period of mourning will end on Monday with a televised fundraising event to support victims, Muyaya said.
Since reports of the massacre emerged, calls for an independent investigation have been mounting.
The president "asked the minister of justice to open an internal investigation without delay and at the same time to work for an international investigation to shed light on this war crime", Muyaya said.
The March 23 movement, or M23, is a predominantly Congolese Tutsi rebel group that was dormant for years.
It took up arms again in November last year and seized the town of Bunagana on the border with Uganda in June.
After a brief period of calm, it went on the offensive again in October, greatly extending the territory under its control and advancing towards Goma.
Kinshasa accuses its smaller neighbour Rwanda of providing M23 with support, something that UN experts and US officials have also pointed to in recent months. Kigali denies the charge.
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