Authorities in Niger state confirmed that gunmen had seized an unknown number of students from the school in the town of Tegina on Sunday, BBC reported.
A teacher told that 150 students were missing, while other reports put the figure at about 200.
Abductions carried out for ransom are increasingly common in northern states.
In February nearly 300 girls were taken by armed men from a boarding school in Jangebe, Zamfara state. Most were later freed.
In the latest incident, witnesses quoted by This Day news website said gunmen riding on motorcycles stormed the town and opened fire indiscriminately. As people fled the attackers went to the Islamic school and seized the children. The school is attended by boys and girls, aged six to 18.
Authorities said two people were shot during the attack and one had since died. A number of people travelling in a car were also reportedly kidnapped.
ZZ/PR