Nine corpses were found trapped inside the migrant boat that went down in the Mediterranean sea on October 8 after the collision off the coast of the Kerkennah islands, the ministry said.
The defence ministry said search operations were ongoing.
At the time of the collision, the ministry said eight migrants drowned and 38 others were rescued, while NGOs and survivors spoke of dozens still missing.
An NGO, the Tunisian Forum for Economic and Social Rights (FTDES), estimates the boat carried between 80 and 100 migrants.
One of the migrants rescued after the tragedy told AFP that 90 people had been on board, hoping to make their way to Italy.
Others who survived the tragedy claimed that their boat had been deliberately struck by the navy vessel.
Military prosecutors are investigating the claims.
According to the International Organization for Migration, there has been a rise in the number of migrants trying to make the perilous sea crossing from Tunisia to Europe since summer.
Small vessels have been heading for the Italian islands of Sicily and Lampedusa.
Flavio di Giacomo, an Italian spokesman for the IOM, told AFP earlier this month that 1,400 Tunisians had arrived in Lampedusa and western Sicily in September alone.
This is compared to 1,200 registered in Italy for all of 2016.
A report by the FTDES last year said that half of Tunisian youths from low-income areas were thinking of leaving the country, and one in three was prepared to do so clandestinely.
It blamed the situation on increasing poverty and unemployment in the North African country.