Militants stormed the Government Girls Science Secondary School in Dapchi, Yobe state, on Monday evening. Locals initially said the girls and their teachers fled the attack.
The jihadists gained worldwide notoriety in April 2014 when they abducted 276 girls from their school in Chibok, in neighbouring Borno state.
Fifty-seven escaped in the immediate aftermath and since May last year, 107 have either escaped or been released as part of a government-brokered deal. A total of 112 are still being held.
"Our girls have been missing for two days and we don't know their whereabouts," Abubakar Shehu, whose niece is among those missing, told AFP.
Also Read
"Although we were told they had run to some villages, we have been to all these villages mentioned without any luck. We are beginning to harbour fears the worst might have happened.
"We have the fear that we are dealing with another Chibok scenario."
According to school staff, there were 710 students at the state-run boarding school, which caters for girls aged 11 and above.
"Nobody is telling us anything officially," he said. "We still don't know how many of our daughters were recovered and how many are still missing.
"We have been hearing many numbers, between 67 and 94."
Police in the state, which is one of three in the northeast Nigeria worst-affected by the Boko Haram insurgency, said they had no reports of abductions following the attack.
Yobe's education commissioner, Mohammed Lamin, said the school had been shut and a rollcall of all the girls who have returned was being conducted.
Some of the girls had fled to villages up to 30 kilometres (nearly 20 miles) away through the remote bushland, he added.
Boko Haram has used kidnapping as a weapon of war since its insurgency began in 2009, seizing thousands of women and young girls, as well as men and boys of fighting age.
Some 300 children were among 500 people abducted from the town of Damasak in November 2014.
Getting accurate information from the remote northeast remains difficult. The army still largely controls access and infrastructure has been devastated by nine years of conflict.
As the issue gained world attention, spawning the hashtag #BringBackOurGirls, the then president Goodluck Jonathan was increasingly criticised for his lacklustre response.
The mass abduction and Jonathan's handling of it was seen as contributing to his 2015 election defeat to Muhammadu Buhari, who promised to bring the Boko Haram insurgency to an end.
But despite Buhari's repeated claims the group is weakened to the point of defeat, civilians remain vulnerable to suicide attacks and hit-and-run raids in the remote northeast.
Security analysts told AFP on Tuesday that government ransom payments to secure the release of the Chibok girls could have given the under-pressure group ideas for financing.
"They need money for arms, ammunitions, vehicles, to keep their army of fighters moving across the borders," said Amaechi Nwokolo, from the Roman Institute of International Studies.
"They're spending a lot of money on arms and logistics.
Disclaimer: No Business Standard Journalist was involved in creation of this content