ONE of Australia's highest paid school principals has broken her silence about a high-profile probe into an alleged $9 million fraud using "ghost pupils" to fund the nation's top indigenous college.

Former Djarragun College head Jean Illingworth took sick leave and was suspended on full pay in March last year pending the outcome of a fraud investigation by Queensland Police.

The former Australian of the Year award winner said in an exclusive interview she felt traumatised by the police probe and "crucified by tall poppy syndrome".

"It is the greatest injustice," said the mother-of-three. "I've been hit with a double whammy, accused of stealing millions when I've never taken so much as a pen.

"And the reputation of the school has been trashed, and funding withheld, and more than a decade of good work in indigenous education destroyed."

Police are investigating the alleged misappropriation of funds by the college due to grossly exaggerating the number of students at the taxpayer-funded school at Gordonvale, south of Cairns.

It is alleged Djarragun wrongly claimed for 250 students over three years, equating to funding of about $36,000 per student.

Detectives are investigating allegations one student, aged 32, was enrolled at the school, ex-students were not taken off the roll after they left, and claims others were fictitious names or "ghost" pupils.

Ms Illingworth broke her after silence returning to Australia after spending the past three months volunteering at an impoverished school in a coastal slum in Northern Mozambique in Africa.

"There is no substance to the allegation of ghost pupils," Ms Illingworth said from her Kuranda home.

"At the time I just laughed, I thought it was ridiculous. But I wish I had not taken it so lightly. I certainly don't now."

She believed an independent audit of the school had cleared her name and "showed no fraud was committed".

"I believe the state has accepted the findings of that audit but I'm not sure about the Commonwealth."

The State Government reportedly identified about $4 million in overpayments. The Djarragun head and chief executive was paid a base salary of $283,500 a year, plus benefits, on a package worth about $300,000  a wage that rivals heads of some of the nation's most expensive private schools

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