Education Minister Simon Birmingham has threatened to withdraw funding to the schools.

The Department of Education and Training formally issued the notifications on Friday following a six month investigation into sackings among senior staff members and principals, allegations of financial mismanagement and concerns about the delivery of the curriculum at the schools.

"I am committed to ensuring that all school authorities meet the requirements of the Education Act to ensure that our taxpayer dollar and any private investment by parents is being spent as intended to benefit Australian students," Mr Birmingham said.

"School governance should be of the highest standard and funding should be used for the benefits of students."

But business manager of the Islamic School of Canberra Mohammed Berjaoui strenuously rejected the accusation that the school is running for profit.

"To get the letter today was a shock for us and I believe the statement is wrong," he said.

"They did auditing on us and they didn't find anything wrong with our finance, management or education standard."

"The fees we set are very very low... How can they say that we are running a business or we are charging our students more than what they are supposed to pay or we are doing it for profit? It is not true."

The six schools in question are affiliated with the Australian Federation of Islamic Councils (AFIC). Only one of them is in Canberra, with others in NSW, Brisbane, Melbourne, South Australia, and Western Australia.

Mr Berjaoui said AFIC "eases pressure" off the government by assisting the Islamic School of Canberra with $1 million each year.

"The money is going into education," he said.

But Mr Birmingham said the government's action does not come lightly.

"All schools must have effective management and accountability arrangements in place to support the best possible education outcomes for their students," he said.

"My focus is always that we, as the taxpayer, get maximum bang for our buck to improve education outcomes of Australian children."

The six schools have been given 28 days to respond to the notices and show how they will comply with the Education Act.

Mr Berjaoui is confident that he will prove the school is "doing no wrong".

"The government's duty is to ask questions and we are going to answer the questions," he said.

"Hopefully the school will continue and we will progress more and more."

The Islamic School of Canberra has been among the top schools in the national capital based on its NAPLAN results in recent years, according to the MySchool website.

Mr Berjaoui is concerned about how the notice will affect the school's reputation.

"The teachers and parents will be worried about the future of our school."

"They are all upset about why our school is targeted and why the government is doing this. It will affect them. Where can they put their children next year if the school closes?"

The Islamic School of Canberra, founded in 2005, is a registered co-educational primary school in Weston. It offers Islamic and academic education to students from kindergarten to year seven (and is seeking accreditation for year eight).

In 2011 the Islamic School of Canberra's former administrator was the subject of a three-year ACT police investigation over forgery charges. However, no charges were laid. The documents related to an application to expand the school.