Salisbury school for girls caters for secondary students with complex needs, including intellectual disabilities, autism, foetal alcohol syndrome, and developmental and behavioural problems.
The school, near Nelson, used to have 80 students, but its maximum has been cut to 30 and it now has only nine students, with two enrolled for next year.
The school fought off an attempt to close it in 2012. The government had decided to shut it down along with Mackenzie Residential School in Christchurch, but keep two others - Halswell Residential College in Christchurch and Westbridge in Auckland.
Salisbury's board of trustees challenged that decision and the High Court ruled that the decision to close it was unlawful.
The former chairperson of the school's board of trustees, Julia O'Connor, said the Education Ministry had assured the school it would remain open. But they were now hearing parents were being discouraged from sending their children there.
"We hear a lot of anecdotes about parents trying to get enrolled and having huge difficulty, feeling actively discouraged," Ms O'Connor told Nine to Noon today.
"We cannot check whether that is an intention on the part of the ministry or whether it is just the system that discourages them."
Julia O'Connor said the school had eight teachers and could easily take more girls.
One problem was that the school was no longer on the panel that checks referrals, so it did not know how many families were interested in sending their children.
A parent told Nine to Noon she had to fight for two years to get her daughter enrolled in Salisbury.
She said her application was turned down three times and it was only after she involved lawyers and politicians that the Education Ministry agreed to let her child go to the school.
The Education Ministry's head of special education, David Wales, said the ministry had no intention of closing Salsibury down.
However a new way of working with children with high needs, the Intensive Wrap Around Services, had reduced the number needing residential care.
"We knew that was going to happen when we set up that service. What we didn't know was the extent to which that would occur."
Mr Wales said now that the ministry can see what the impact has been on Salisbury, there was work to do to figure how to best use its facilities for those girls who most need it.
A New Direction - Katy Gosset takes a tour of Salisbury school as the pupils return from their holidays.