The attack and abductions early on Friday took place at St Mary's School, a Catholic institution in Agwara local government's Papiri community, said Abubakar Usman, the secretary to the Niger state government.
He did not disclose the number of students and staff abducted, nor who might be responsible for the attack.
Local media broadcaster Arise TV said 52 schoolchildren were abducted.
The Niger State Police Command said military and security forces had been deployed to the community.
It described St Mary's is a secondary school, which serves children between the ages of in 12 and 17.
The statement by the secretary to the Niger state government said the incident occurred despite prior intelligence warning of heightened threats.
"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," it said.
The abductions took place days after gunmen on Monday attacked a high school and abducted 25 schoolgirls in the neighbouring Kebbi state, in Maga, 170km from Papiri.
One the girls later escaped and is safe, the school's principal said.
Nigeria's President Bola Tinubu postponed his trip to this weekend's Group of 20 summit after promising to intensify rescue efforts.
No group has claimed responsibility for the attacks in Niger and Kebbi state, but analysts and locals say gangs often target schools, travellers and remote villagers in kidnappings for ransom.
Authorities say the gunmen are mostly former herders who have taken up arms against farming communities after clashes between them over strained resources.
Abductions have come to define the insecurity prevailing in Africa's most populous nation and the painful consequences.
At least 1500 students have been abducted in the region since Boko Haram jihadi extremists seized 276 Chibok schoolgirls more than a decade ago.
But bandits are also active in the region, and analysts say gangs often target schools to gain attention.
Analysts and residents blame the insecurity on a failure to prosecute known attackers, and the rampant corruption that limits weapons supplies to security forces while ensuring a steady supply to the gangs.
