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.
Nigeria has faced a renewed wave of attacks by armed groups in recent days, including the kidnapping on Monday of more than 20 schoolgirls, who the BBC has been told are Muslim, from a boarding school in neighbouring Kebbi state.
A church was also attacked further south, in Kwara state, with two people killed and 38 abducted while the service was being broadcast online.
President Bola Tinubu has postponed his foreign trips - including this weekend's G20 summit in South Africa - in order to address these security issues.
Police said armed men - locally known as bandits - stormed St Mary's School on Friday at about 02:00 local time (01:00 GMT) and abducted students from their hostel.
Fear and uncertainty have gripped the area as families wait for news.
"Everybody is weak... it took everybody by surprise," local resident Dominic Adamu told the BBC.Mr Adamu, whose daughters attend St Mary's School but were not abducted, added: "People are complaining about the state of security in our country."
One distressed woman tearfully told the BBC that her nieces, aged six and 13 were kidnapped."I just want them to come home," she said.
The authorities in Niger state said the school, attended by both girls and boys, had disregarded an order to close all boarding facilities following intelligence warnings of a heightened risk of attacks.
"Regrettably, St Mary's School proceeded to reopen and resume academic activities without notifying or seeking clearance from the state government, thereby exposing pupils and the staff to avoidable risk," they said in a statement.
The school has not commented on that claim.