The school had raised the issue during a meeting with Ms Parata, and a report about the vulnerability of girls at special needs schools had been earlier published for the Education Ministry and police.
"The minister's decision failed to have regard to available warning signals raised by and on behalf of the [school] trustees about greater levels of risk of abuse in a co-educational setting," Justice Dobson said.
A spokeswoman for Ms Parata said the minister was at a function last night and would not get a chance to read the findings before the Herald went to press.
Two weeks before Ms Parata confirmed the school's closure, representatives from Salisbury told her of the risks.
One trustee who had run a residential facility told her "we never mix them [boys and girls] unless they're in wheelchairs", said the school's lawyer, Mai Chen.
There was a horrendous record of sexual and physical abuse at schools for the intellectually impaired.
In one study, all but two students at a boys' school were found have been victims of abuse, Ms Chen said.
Salisbury School had lost confidence in Ms Parata and her officials, she added.
Twenty-two girls were to be affected by closing Salisbury.
The aim was to put some into mainstream schools, with those needing residences having the option of moving to Halswell.
In court, Ms Parata's legal team argued the school's concerns did not "precisely" relate to the proposal for bringing girls to Halswell.
Justice Dobson, however, said: "Those are, with respect, inappropriately technical distinctions to apply in assessing so important an issue."
Green Party education spokeswoman Catherine Delahunty said Ms Parata was "out of her depth".
Minister's gaffes
Ms Parata's troubles in 2012:
*Caused a public outcry after proposing to increase class sizes.
*Angered teachers at a conference when she told them - in what was seen as a condescending comment - to pronounce children's names correctly.
*Came under fire for proposals to close or merge several Christchurch schools.
