Maman Sidikou said he was "deeply shocked" at the violence. Another 117 people were wounded and one Congolese officer was killed, he said in a statement.
Thirty-nine gravely wounded Burundian refugees were evacuated by helicopter to the city of Bukavu, the UN peacekeeping mission in Congo said.
Yesterday's clashes erupted in Kamanyola in Congo's South Kivu province when Burundian refugees and asylum-seekers protested the expulsion of four of their countrymen from Congo, Sidikou said, citing "credible reports" received by the peacekeeping mission. The death of the Congolese army officer led to "the escalation of violence."
Congo's military could not immediately be reached for comment.
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Roughly 44,000 refugees from Burundi are sheltering in Congo. Many fled political violence at home in 2015, when President Pierre Nkurunziza successfully pursued a disputed third term amid deadly protests.
Of the people killed in yesterday's clashes, 15 were women, the commander of the Pakistani battalion of the UN peacekeeping mission, Waquara Yunusi, told The Associated Press.
The Congolese government, the UN refugee agency and the UN peacekeeping mission in Congo "have deployed teams on site to shed light on everything that happened," said the coordinator of the UN Communications Group in Congo, Florence Marchal.
Residents in the area said the killings occurred after some Burundian refugees went to the bureau of intelligence in Kamanyola to inquire about four detained refugees. Congolese soldiers responded with gunfire when some of the refugees hurled stones, said refugee Aline Nduwarugira.
It was not immediately clear why the four refugees had been detained.
Another witnesses, Alfred Rukungo, said Congolese soldiers continued shooting into the crowd even after some refugees were wounded.
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