The Yobe state government issued a statement on Thursday that retracted an earlier one that some of the missing girls had been rescued by the military.
"We have now established that the information we relied on to make the statement was not credible. The Yobe state government apologises for that," said Abdullahi Bego, spokesman for Yobe Governor Ibrahim Gaidam.
Late on Wednesday, Bego had said some girls had been "rescued by gallant officers and men of the Nigerian army from the terorrists who abducted them".
Bego did not give a specific number of those saved.
Police said on Wednesday that 111 girls from the state-run boarding school in Dapchi, in Yobe state, were unaccounted for following an attack by the armed group on Monday night.
But exact figures have been difficult to confirm.
On Thursday, parents said 101 children were still missing, The Associated Press reported, while unidentified sources told Reuters 91 were gone.
The students were reported to have fled the attack with their teachers at the sound of gunfire.
More than 20,000 people have been killed and two million others forced to flee their homes in northeastern Nigeria since Boko Haram launched a campaign in 2009 aimed at forming a breakaway state.
Over the years, the armed group has kidnapped thousands of adults and children.
Nigerian President Muhammadu Buhari recently said the era of Boko Haram violence "is gradually drawing to end".
However, the group continues to launch attacks in the country's northeast, and its leader remains at large.