Senior students are no longer attending class at Moerewa School in Northland following the arrival of a commissioner appointed by Education Minister Hekia Parata.
The minister sacked the school's board on Monday, after Year 11 to 13 pupils turned up on the first day of term, contrary to a directive that they be enrolled elsewhere.
The school tried to formalise its senior class last year and until now has been run as a satellite unit of an Auckland school.
The ministry says it had no option but to take action, because the standards of learning at the school are not good enough and there are serious issues with assessments.
Ms Parata says Moerewa cannot give older students the quality education they deserve, whereas nearby secondary schools can.
A parent with a son in the senior unit says the students are now waiting at home, while family negotiate with the local kura kaupapa to take them on as a group.
However, he says parents are worried that the ministry may try to block that.