The head of the Prime Minister's department is refusing to release his secret report into the way a $100 million pre-election sports grants program was administered but has conceded the program had "significant shortcomings".

Key points: The Government has refused to release Phil Gatejens' report into the sports grants program

The Government has refused to release Phil Gatejens' report into the sports grants program Mr Gaetjens has provided a summary of his report to a Senate inquiry examining the pre-election program

Mr Gaetjens has provided a summary of his report to a Senate inquiry examining the pre-election program He said there were shortcomings in decision making but Bridget McKenzie wasn't "unduly influenced" by marginal electorates

The Department of Prime Minister and Cabinet secretary Phil Gaetjens late on Friday made his first public intervention into a saga that has weighed heavily on the Federal Government for more than a month.

In a six-page submission to a Senate review into the Government's handling of the program, Mr Gaetjens revealed then-sports minister Bridget McKenzie told him she had never seen the now-infamous colour-coded spreadsheet that advisors used when assessing applications by electorate.

It came a day after the Senate hearing heard conflicting testimony about the eligibility of grants the Coalition handed out before last May's election.

Mr Gaetjens is a former chief of staff to Scott Morrison but from when the Prime Minister was the treasurer.

In his secret report, which Mr Morrison commissioned, Mr Gaetjens assessed Senator McKenzie's handling of the program when she was sports minister in 2018 and early 2019.

Bridget McKenzie quit Cabinet after Phil Gaetjens gave his report to the Prime Minister. ( ABC News: Sean Davey )

His investigation followed an auditor-general's finding that the $100 million program for community sports infrastructure had a bias towards marginal government seats and electorates that the Coalition was targeting in last year's election.

Mr Morrison has previously asserted that the Gaetjens report contradicted the auditor's finding but has resisted political pressure to release the full report.

Mr Gaetjens' Senate inquiry submission said the full investigation he completed for Mr Morrison remained "subject to the rules of Cabinet confidentiality".

His summary document said there were "significant shortcomings" in the way Senator McKenzie decided on the grants.

Projects in Liberal-held seats averaged about $40,000 more than those in Labor seats. ( ABC News: Matthew Doran )

Mr Gaetjens identified a "lack of transparency" for applicants and the divergence between projects recommended by the assessment body Sports Australia and Senator McKenzie.

But he said he disagreed with the auditor-general's finding on the question of bias.

"I did not find evidence that the separate funding approval process conducted in the Minister's office was unduly influenced by reference to 'marginal' or 'targeted' electorates," the report states.

Mr Gaetjens also said he had looked into the spreadsheet that was leaked to the ABC, and whether it had an impact on decision making.

He said Senator McKenzie advised him "she had never seen the advisor's spreadsheet" and that neither she nor her staff "based their assessments on it".

Senator McKenzie quit Cabinet, after Mr Gaetjens handed his confidential report to the Prime Minister, for failing to disclose her membership of a gun club that received funding.