Thirty-three people were killed and 15 injured in clashes with guards, police chief Bernardino Rafael told a press conference.
About 150 more fugitives have since been recaptured, he added.
Protests erupted on Monday in response to Mozambique’s highest court confirming that the ruling Frelimo party, in power since 1975, had won October’s presidential elections.
Mr Rafael said groups of anti-government protesters had approached the prison in the capital Maputo on Wednesday. Prisoners used the unrest to knock down a wall and escape, he said.
Mozambique has been rocked by unrest since disputed elections in October. Official results showed the ruling Frelimo’s candidate for president, Daniel Chapo, winning.
Fresh protests erupted on Monday, when the constitutional court ruled that Chapo had won the election, while revising his margin of victory downwards.
Initial results in October said Daniel Chapo gained a 71% share of the vote to his main rival Venâncio Mondlane’s 20%. The court has now ruled that he won 65% to Mondlane’s’s 24%.
A BBC reporter found Maputo was like a ghost town on Christmas Eve, with almost all businesses shut and people staying at home to avoid being caught up in the worst unrest in the city since Frelimo first rose to power in 1975.
Frelimo’s offices, police stations, banks and factories have been looted, vandalised and set ablaze around the country. Since Monday, at least 21 people have been killed in the unrest, the interior minister said late on Tuesday.
Mondlane, who has since fled Mozambique, had been calling on his supporters to demonstrate against what he said was a rigged vote.
In a weekend social media message, he said there could be a “new popular uprising” if the result was not overturned.
About 150 people have been killed in three months of protests since the elections.
