South Australia's Department for Education has been ordered to apologise to a Muslim family over an Adelaide public school's handling of their attendance of Friday prayers during teaching hours.

Key points: The family of refugees felt "personally attacked" by the school's response, the ombudsman found

The family of refugees felt "personally attacked" by the school's response, the ombudsman found The father believed his children were being expelled because of their attendance of prayers

The father believed his children were being expelled because of their attendance of prayers The ombudsman has recommended the school change its practices

State ombudsman Wayne Lines has released the findings of an investigation into the matter, recommending the department apologise to the family and change school attendance policies to allow for students to attend Friday prayers.

Mahmoud Amirat and his two sons attended a mosque for up to 90 minutes every Friday, during teaching hours at the Adelaide Secondary School of English where the boys were enrolled in 2017.

Mr Amirat and his children were refugees who did not speak fluent English at the time.

In a letter written only in English, the school expressed concern the children "missed part of their lesson".

However, the ombudsman found the West Croydon school inadvertently gave Mr Amirat the impression that his children were being expelled because of their religious practice.

Mr Lines expressed concern that the school "did not show greater understanding of the cultural significance of engaging in Friday prayer at a mosque".

"[This] was not a situation where a parent was removing a child for an improper reason, instead, the absences were for genuine religious and cultural reasons," the report stated.

"[Despite] the school's awareness of the children's regular absences, it did not appear to negotiate an alternative arrangement … in the circumstances of this case, it was inappropriate and unreasonable to rigidly insist that the children attended all their Friday lessons."

The ombudsman reported that while school had prayer rooms on-site, Mr Amirat and his children felt "personally attacked and embarrassed" by the school's response.

School said enrolment 'had been terminated'

In October 2017, the school's principal met with Mr Amirat with the aid of an Arabic translator.

The principal suggested that his two children be moved to an adult campus, Thebarton Senior College, since the eldest child was then almost 18 years old.

During the meeting, the principal also stated concerns about the Friday absences, according to the ombudsman's report.

Ombudsman Wayne Lines found the school needed to improve the way it communicated. ( ABC News: Isabel Dayman )

Soon afterward, the school sent a letter to Mr Amirat, reiterating the concerns about the Friday absences and advising that the children's enrolment would be ended.

Mr Lines said the letter was written in English, with no translation.

He said the school had concerns about one of the student's "disruptive" behaviour, and had contacted Mr Amirat over the matter, again advising the boy's enrolment "had been terminated".

The ombudsman accepted that the school wanted to move the children to the adult campus because of the age of the eldest, but found the school never "clearly stated this".

Mr Amirat's son said he had felt "scared" when he got into trouble at school for attending Friday prayers.

"I felt alone, and no-one is helping me, and no-one is supporting me," he said.

"I was scared, me and my brother … my knees were shaking."

Speaking via his son as translator, Mr Amirat said his family's treatment by the school had made him question his belief in Australian freedoms.

"Coming to Australia, we thought it was a freedom (sic) country and you can practise your religion," said Mr Amirat.

"After [the ombudsman's] decision we are happy."

The ombudsman recommended the Department for Education apologise to the family on the school's behalf and update attendance procedures to allow for students to be absent from school to attend Friday prayers.

The report stated the department had accepted the recommendations.

The ABC has contacted the department and the school for comment.