A church was also attacked in the south-western Kwara state, with two people killed and 38 abducted while the service was being broadcast online.
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 an unconfirmed number of students from their hostel.
Fear and uncertainty have gripped the area as families wait for news.
The 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.
"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.

