"Many girls were abducted by the rampaging gunmen who stormed the school in a convoy of vehicles," said Emmanuel Sam, an education official in the town of Chibok, where the attack took place yesterday.
The attackers are suspected to be members of Boko Haram, a radical Islamist group whose name means "Western education is forbidden".
It has repeatedly attacked schools in the northeast during an insurgency that has killed thousands since 2009.
He said soldiers had been deployed to provide extra security ahead of yearly exams, but the gunmen "subdued the soldiers and took the girls away".
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He was not able to provide an estimate of the number of girls abducted.
In an attack earlier this year in Borno state, witnesses said Boko Haram gunmen surrounded a girls' school, forced the students to leave and ordered them to immediately return to their villages.
Sam spoke in Borno's capital Maiduguri where he said he fled after the attack at the Government Girls Secondary School in Chibok.