As many as 110 girls have been missing since Monday when armed militants stormed the school.
However, the Nigerian government is yet to release an official list of those missing.
The ministry is basing the latest number on briefings with the school principal and the Commissioner for Education, reported CNN.
Boko Haram militants kidnapped nearly 300 girls from a school in Chibok in April 2014, setting off global outrage. Many of the Chibok girls were freed after negotiations, but more than 100 remain in captivity, their whereabouts unknown.
Suicide attacks carried out by the dreaded insurgent group have claimed more than 20,000 lives and displaced at least two million people, according to Nigerian vice-president Yemi Osinbajo.
The group is also active in the neighbouring countries of Cameroon, Chad, and Niger. (ANI)