Police and soldiers opened fire as the refugees protested over a plan to send some of them home, local activists said.
Troops shot dead 34 Burundian refugees in clashes in Kamanyola in eastern Democratic Republic of Congo, local officials in the eastern province of South Kivu said Saturday.
A Burundian refugee said that more than 30 had been killed and at least 100 wounded in the violence on Friday.
Interior ministry official Josue Boji said troops had tried to disperse the refugees by "firing in the air but were overwhelmed" when the group responded by throwing stones.
Boji said the clashes began after a group of refugees overran a jail run by the country's domestic intelligence agency to demand the release of four Burundians who had been arrested for expulsion on Wednesday night.
"There are 34 dead and 124 wounded among the Burundian refugees," he said, revising upwards an earlier toll of 18 dead plus one DR Congo soldier.
Boji had warned earlier that the toll could rise further, as the refugees took the bodies of other victims to the UN camp at Kamanyola.
A spokeswoman for MONUSCO, the UN's peacekeeping mission in the country, gave a toll, which was also provisional, of 18 dead and 50 injured.
A Burundian refugee said: "I saw people falling down, men, women and children who were completely unarmed.
"So far, we have counted 31 dead and at least 105 injured, 15 of them seriously," the refugee said.
Burundi's foreign minister, Alain-Aime Nyamitwe, on Twitter described the incident as a "shooting" and said "explanations are needed."
Tens of thousands of Burundians have fled to the eastern DR Congo to escape a wave of violence that unfurled in 2015 after Burundian President Pierre Nkurunziza sought a fiercely contested third term in office.
Overall, the violence in Burundi has claimed between 500 and 2,000 lives, according to differing tolls provided by the UN or NGOs and more than 400,000 Burundians have fled abroad.
Around 36,000 are in DR Congo, mainly in the overcrowded camp of Lusenda, in the east, or several transit camps.
On September 4, the UN released a report accusing Burundi's government of crimes against humanity, including executions and torture, and urged the International Criminal Court (ICC) to open a case "as soon as possible".
Burundi's government firmly rejected the allegations, accusing the UN investigators of being "mercenaries" in a Western plot to "enslave African states".