A statement released by Nyusi’s office was an update from earlier reports by officials who had placed the death toll at 98.
President Nyusi was saddened by the tragedy and has directed Mozambique’s transport minister to investigate the matter, the statement said.
"The Mozambican Government will meet tomorrow to assess the situation and take necessary measures to minimize the impact of this incident," Nyusi’s office said.
An official from Mozambique’s Maritime Transport Institute, INTRASMAR, described the ferry as an overloaded fishing boat which was not licensed to transport people.
130 people were aboard the unlicensed vessel, INTRASMAR said.
Lourenco Machado, an administrator of the maritime transport institute, gave an update on state television. He said the boat was ferrying people from Lunga in Nampula province to Mozambique Island on Sunday.
Initial reports indicate that the boat was hit by a tidal wave, Machado said.
Menque Amade, a crew member who survived, spoke to national broadcaster TVM on Monday. He said, "water filled the boat... and the tragedy happened."
The Office of the Secretary of State for Nampula province released a statement on Monday which said the passengers were reportedly fleeing a cholera outbreak, adding that 10 people had been rescued while nearly 20 were still missing.
The information on the cholera outbreak was inaccurate and caused panic, according to Jaime Neto, Nampula’s secretary.
Neto said children were among the victims of the ferry sinking.
Mozambique, one of the world's poorest, has recorded almost 15,000 cases of cholera and 32 deaths since October, according to government data.
Nampula is the worst affected region, accounting for a third of all cases.
Locals say health authorities recently stepped up outreach and prevention efforts.
But the increased medical presence caused a scare among some residents, pushing a number of them to flee, they said.
In recent months, the province has also received a large influx of people fleeing a wave of jihadist attacks in its northern neighbor of Cabo Delgado.
Some information for this article was sourced from Reuters and Agence France-Presse.