The Christian Association of Nigeria said 303 students and 12 teachers were taken from on St Mary's School in Papiri, Niger state - substantially more than previously estimated.
It said the figures have been revised upwards "after a verification exercise".
The kidnapping comes amid a surge of attacks by armed groups. The revised number of people taken surpasses the 276 abducted during the infamous Chibok mass abduction of 2014.
Local police said armed men stormed the school at around 02:00 local time (01:00 GMT) on Friday morning, abducting students who were staying there.
Dominic Adamu, whose daughters attend the school but were not taken, told the BBC: "Everybody is weak... it took everybody by surprise."
One distressed woman tearfully told the BBC that her nieces, aged six and 13, had been kidnapped, adding: "I just want them to come home."
Police said that security agencies were "combing the forests with a view to rescue the abducted students".
It was initially reported that 215 pupils had been taken - but that figure has since been revised upwards. The new number is believed to be almost half of the school's student population, the news agency AFP reports.
Authorities in Niger state said the school had disregarded an order to close all boarding facilities following intelligence warnings of a heightened risk of attacks.
They said in a statement the move exposed pupils and staff to "avoidable risk". The school has not commented on that claim.
