Key NAPLAN results have plunged in the Aboriginal school on Cape York at the centre of a bitter row between the Queensland government and indigenous leader Noel Pearson, who is championing back-to-basics education reform.

Aurukun State School was closed for a tumultuous month last year after violence by youth gangs forced the evacuation of teachers. In the fallout, Mr Pearson’s Good to Great Schools Australia organisation pulled out of a program to lift literacy and numeracy, claiming this had been sabotaged by a “takeover” by Education Queensland.

The reading scores of Year 3 students at the school have since halved, the latest NAPLAN data shows. This means the classmates of the eight-year-olds who were reading at above the national minimum standard two years ago are barely at preschool levels of comprehension now, the scores crashing from 335 in 2015 to 148.

The grammar and punctuation score for the Year 3s went from 216 in 2015 to a low 80; writing scored at 192, down from 275 two years ago while the Year 5s have flatlined on some measures. But Education Queensland says participation in NAPLAN tests has increased from 37 per cent to 67 per cent in that time.

“I’m just completely heartbroken about the loss of opportunity for those kids,” Mr Pearson said.

Grandmother Phyllis Yunkaporta, who has a grandchild at the school, where she works as a teacher’s aide, said it had “gone haywire” since GGSA withdrew. “Our kids are out of control … they are outside most of the time running amok,” she said.

But parents and citizens’ ­association president Stuart Marquardt insisted there was stronger engagement between the school and the remote community than there had been when GGSA was involved.

Education Queensland assistant director-general Selwyn Button said GGSA had advised last November that it would cease support for the school. Attendance had increased from 52 per cent in 2015 to 59 per cent for the first term of this year, he said.

Aurukun, 2400km north of Brisbane, was a proving site for Direct Instruction teaching of ­indigenous children. Good to Great Schools Australia, which operates Mr Pearson’s Cape York Aboriginal Academy, ran the program in partnership with the state education department.

But in May last year, public order problems came to a head in the township of 1200 when the principal and his wife were threatened by machete-wielding youths during a carjacking.

Education Queensland ordered the evacuation of the school’s 25 teachers. They returned only to be pulled out a second time when more trouble flared, forcing the government to close the school until police regained control. NAPLAN testing for 2016 was cancelled.

Mr Pearson has now accused the outgoing director-general of Education Queensland, Jim Watterston, of “exploiting” the crisis to oust GGSA.

“My dispute with Watterston is profound, but is secondary to the welfare of these children,” he said. “I held my peace this year to allow Watterston and his department to do the right thing by them. Instead, Watterston washed his hands of that school, having caused so much damage last year. Now he’s walking away from the ruins.”

Mr Pearson’s allegations were put to Education Queensland but Dr Watterston did not respond. He announced on Wednesday that he was leaving to become dean of the Melbourne Graduate School of Education at the University of Melbourne.

Education Minister Kate Jones said Dr Watterston’s departure was unrelated to the ­Aurukun dispute, which was also the subject of a complaint to the Queensland Crime and Corruption Commission by Mr Pearson alleging that Dr Watterston was behind an “unlawful and improper” release of confidential audits of the Cape York Academy to the ABC, under Right to Information provisions.

“We are continuing to work with the school, community and parents to improve the education performance at the school,” Ms Jones said.

“We have seen encouraging results when it comes to the latest Year 5 NAPLAN data.”

A spokesman for the CCC said it had made “procedural recommendations” to Education Queensland about information access and security.