The vessel was an overloaded fishing boat and was not licensed to transport people, Lourenco Machado, an administrator of INSTRASMAR, said on state television on Monday.
"On Sunday we registered a maritime incident where at least 94 people died when a barge carrying 130 people capsized. We have recovered 94 bodies and 26 are missing," he said.
The boat was ferrying people from Lunga in Nampula province to Mozambique Island, he said, adding that initial reports indicated that it was hit by a tidal wave, Reuters reported.
The passengers were fleeing a cholera outbreak, said state broadcaster TVM, citing another local maritime administrator.
Jaime Neto, secretary of state for Nampula province, also said that the passengers were fleeing cholera, according to the British Broadcasting Corp (BBC).
"Because the boat was overcrowded and unsuited to carry passengers, it ended up sinking," he said, adding that many children were among the dead.
Videos posted on social media X showed many bodies lying on a beach and some people carrying the bodies of children.
Mozambique and other countries in Southern Africa have been battling cholera outbreaks since last year.