The boat was travelling from Uganda, which sits across the lake from the Democratic Republic of Congo, and was transporting around 300 people who were returning home from refugee camps.
"It is with deep sorrow that we confirm to the nation the death of 251 of our compatriots who had boarded the boat from the Ugandan side of Lake Albert," government spokesman Lambert Mende told reporters.
Congolese President Joseph Kabila proclaimed three days of public mourning starting today "to show solidarity and compassion with the entire Congolese nation", Mende said.
"They have unfortunately not followed the traditional method of repatriation, a method that involves the host country, in this case Uganda, the country of origin, the Democratic Republic of Congo, and the UN High Commission for Refugees," he said.
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UNHCR said it was one of two boats leaving Hoima district on the eastern shore of the lake on Saturday.
The body count has mounted rapidly in recent days. Initial reports on Saturday said 20 had died, but this increased to 98 by Monday and 107 on Tuesday, including 57 children.
Saturday's disaster happened just days after Congolese authorities launched a campaign to enforce the wearing of life jackets aboard all boats on the nation's many waterways.
Uganda remains a haven for refugees, according to UNHCR. While most of the new arrivals have fled conflict in South Sudan, the country is still home to 175,000 Congolese among a total of almost 329,000 refugees registered at the end of February.