CONFLICT of interest issues have been highlighted in an audit of a grant program that awarded $2.4 million to a company linked to Leichhardt MP Warren Entsch's former campaign manager.

The Australian National Audit Office probe's Regional Jobs and Investment Package findings flew largely under the radar after they were released during the Melbourne Cup.

Concerns were uncovered about the $224.3 million program's national rollout, with some applications not soundly assessed and eligibility requirements not applied in full.

"Requests for co-funding exemptions were not appropriately considered and conflict of interest management was not to a consistently appropriate standard," the report states.

The investigation followed controversy over a $2.4 million handout to QRX Group 1 - a Cairns company planning to build Northern Australia's first pharmaceutical distribution and manufacturing centre.

The Cairns Post last year revealed the company was one-third owned by the wife of Mr Entsch's former campaign manager, Trent Twomey.

Mr Twomey was also chosen to chair the local committee setting parameters for what industries should get funding.

He had no role beyond the industry selection process and no hand in the assessment of specific project proposals.

The proponents behind QRX Group 1 have since abandoned the scheme.

The audit found "no bias clearly evident in the assessment and decision-making processes" across the program.

However, it did reference the QRX case.

"A company, whose director was the spouse of the committee chair, was approved for funding and another director of the same company was a business partner of the chair," it said.

"The applicant had not declared the conflict at the application stage. The chair had returned a blank declaration of consent by family members.

"The conflict was not declared once the committee was operational, even though the local planning committee terms of reference require that 'the declaration of conflicts of interest must be a standing agenda item for all committee meetings."

Mr Twomey did not wish to comment, but Mr Entsch said the region was worse off for QRX Group 1's disbandment.

"The group I appointed identified the industries - tourism, health, et cetera, and said that's where we need to draw applications," he said.

"They did not nominate projects, they did not set the criteria, they did not see one of the applications that went through.

"They had nothing to do with application assessment and certainly nothing to do with the final approvals."