The organisation that assessed grants at the centre of the sports rorts scandal warned then-minister Bridget McKenzie there were risks if she approved cash splashes independently of its advice.
But it says ultimately it was not unusual for a minister to have the final decision on such grants.
That comes as Labor has suggested a brief approving the third and final round of grants may have been improperly backdated.
The auditor-general found the controversial $100 million program favoured coalition-targeted seats before the May 18 election.
The grants were paid by Sport Australia, which is overseen by the Australian Sports Commission.
Commission chair John Wylie told a Senate committee investigating the grants on Thursday that Sport Australia assessed applications using a thorough, independent and merit-based process.
But the program was very clearly designed to give Senator McKenzie the decision-making and approval role, he said.
"It was ... ultimately the minister's prerogative to make decisions as the minister saw fit," Mr Wylie said.
He told senators it was not appropriate for Sport Australia to comment on the minister's decision-making process.
However, acting chief executive Robert Dalton told the hearing Sport Australia was not aware of what assessment process the minister might have gone through.
The organisation twice raised concerns with the minister's office over email - in December 2018 and March 2019 - about the risks involved in making decisions independently of its advice.
Mr Dalton said the commission was comfortable at the time that those risks were being managed because it had informed the minister's office of them.
It had not been alarmed at the prospect the minister had the final sign-off because that had happened before.
"This was not something that was new, that sent alarm bells. We actually had had precedent before on this particular process," he said.
The auditor-general found it was not evident what legal authority Senator McKenzie had to approve the grants.
The organisation also confirmed it received final advice from the minister's office about the third round of grants under the program at 8.46am on April 11, less than 20 minutes after the parliament had been prorogued and put into caretaker mode ahead of the election.
The brief had been dated April 4, despite Senator McKenzie's office sending a list of grants she intended to approve to Mr Morrison's office on April 10.
It was one of 136 emails between the prime minister and Senator McKenzie's office about the scheme, according to information provided by the auditor-general in response to a question on notice on Wednesday.
The timeline prompted questioning from Labor in parliament about whether the approval document had been backdated.
Mr Morrison stressed Senator McKenzie had been the "decision-maker" for the grants, not him.
"There was no authorisation provided by me as prime minister on the projects," he told parliament on Thursday.
"Those authorisations were provided on the 4th of April, according to the approval of the brief by Senator McKenzie, on that date, as advised by Sport Australia."
Senator McKenzie was forced to quit after she was found to have broken ministerial rules by not declaring potential conflicts of interest relating to gun club memberships.
Labor leader Anthony Albanese also accused Mr Morrison of being the "MasterChef of cooking the books when it comes to the corrupt sports rorts scheme", after a football club facility in the prime minister's own electorate was given funding after it had been built.
"The project was approved for funding by the then-minister for sport based on its assessed eligibility by Sport Australia," Mr Morrison said.
Australian Associated Press