The attackers reportedly arrived at the school in Chibok, Borno state, late last night, and ordered the hostel’s teenage residents on to lorries.
The attackers are believed to be from the Islamist group, Boko Haram, whose militants frequently target schools.
On Monday, bombings blamed on the group killed more than 70 people in the capital, Abuja.
Boko Haram, whose name means “Western education is forbidden” in the local Hausa language, has been waging an armed campaign for an Islamic state in northern Nigeria.
The exact number of missing students had yet to be established, as some of the girls had managed to return to their homes.
“Many girls were abducted by the rampaging gunmen who stormed the school in a convoy of vehicles,” AFP news agency quotes Emmanuel Sam, an education official in Chibok, as saying.
Another witness, who requested anonymity, told AFP that gunmen overpowered soldiers who had been deployed to provide extra security ahead of annual exams.
The schoolgirl said the men loaded the food items in the store into a truck and ordered some of the girls to climb in.
The other girls were packed into a bus and two other trucks, one carrying sacks of food and the other petrol.
The girl said the convoy had passed about three villages when the truck she was in developed a fault and was forced to slow down.
This gave her and about 10 to 15 other girls the opportunity to jump off and escape into the bush.
Nigerian media reported that two members of the security forces had been killed, and residents said 170 houses were burnt down during the attack.
Boko Haram emerged as a critic of Western-style education, and its militants frequently target schools and educational institutions.
This year, the group’s fighters have killed more than 1,500 civilians in three states in north-east Nigeria, which are currently under emergency rule.
The Nigerian government recently said that Boko Haram’s activities were confined to that part of the country.
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