The state government spends $3.9 million a year on the four Koori schools - 16 per cent of indigenous education funding - even though they educate fewer than 1 per cent of Koori students in government schools.

The Victorian Education Department temporarily shut the Ballerrt Mooroop College in Glenroy this week because it had just one remaining full-time student and 13 staff.

''Because funding for Ballerrt Mooroop College stands at more than $1 million, the department has decided it cannot justify the spending of that amount of money on just one student,'' a spokeswoman said.

An independent review of the four Koori schools, which are located in Glenroy, Morwell, Swan Hill and Mildura, will examine whether there is still a need for them, whether the concept was appropriate or flawed, whether they improved student outcomes and if they provide value for money.

Indigenous educator Chris Sarra said it was unfair to plough so much money into Koori schools when the vast majority of indigenous students received a tiny fraction of that amount at mainstream schools.

Victoria's Koori pathways schools, which are intended to reconnect disengaged students with mainstream schools, opened in 2009 after the former Victorian College of Koori Education was closed following a scathing report by Dr Sarra.

Dr Sarra said in the report the college, which had four campuses, had become a ''dumping ground'' for difficult students.

He recommended the funding be used to establish early learning centres to prepare indigenous children for primary school and to help mainstream schools cater for the needs of indigenous students.

However, Dr Sarra said the current model was ''quite contrary'' to his recommendations.

''I believed then and I absolutely believe now that Koori communities and children deserved much much better,'' he said.

''What was clear was that an extraordinary and disproportionate amount of resources were being ploughed into a small number of kids, while others who had made a choice to go to a mainstream school were left unattended.''

The Koori schools had a combined enrolment of only 65 students last year.

Woolum Bellum College in Morwell received more government funding per student than any other school in the state, according to the My School website.

The school received $82,277 per student in combined state and federal funding - eight times the state average of $10,946 a student.

All four Koori schools were in the top six government-funded schools per student in the state.

The school attendance rate was just 44 per cent last year at Payika College, Swan Hill, 56 per cent at Woolum Bellum College, 59 per cent at Two Rivers College, Mildura, and 64 per cent at Ballerrt Mooroop College.

Two Rivers College was the only Koori school to post NAPLAN results on the My School website. It performed substantially below the national average in all categories.

Victorian Aboriginal Education Association general manager Lionel Bamblett said he believed the Koori schools model was flawed because it focused on trying to get students back into mainstream schools.

''A lot of these kids aren't going to go back into the normal classroom, they are old heads on young bodies,'' he said. The schools should be retained but should focus on early years learning and helping older students obtain skills they need to get a job or go to TAFE.

The independent review will present initial findings to the department on March 26.