"What then happened subsequently was that late applications were taken on board,which were ineligible under the guidelines,"Mr Boyd said.
"Amendments were made to four existing applications,which were ineligible under the guidelines,and they were funded."
Mr Boyd said the time taken for the decisions also meant eight projects had been completed before the funding agreement had been signed,which meant they were also ineligible.
"And there were 270 or something where the project had started before the funding agreement was in place,which is also ineligible under the program,"he said.
"So we get to around 43 per cent of those which were awarded funding,by the time the funding agreement was signed,were ineligible."
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Mr Morrison has contrasted his government's scheme with previous Labor schemes that gave money to projects ruled ineligible.
"The Auditor-General found that there were no ineligible projects,"the Prime Minister said on radio station 3AW on January 20.
After the hearing,a government spokesperson said:"As the ANAO’s own report highlights,“no applications assessed as ineligible were awarded grant funding” and that point was reiterated by the ANAO during the Committee hearing."
The Senate inquiry also heard ministerial advisers used 28 different versions of a colour-coded spreadsheet to allocate money in a process that could not show why each project received the cash.
The federal Auditor-General revealed the process in new testimony on the sports funding affair after a political scandal that forced the resignation of former Nationals deputy leader Bridget McKenzie.
Audit officials also confirmed Prime Minister Scott Morrison's staff made representations to Senator McKenzie's advisers about which projects should gain funding.
But the officials said Senator McKenzie was the final decision-maker and representations from Mr Morrison's office did not always lead to approval.
"It wasn't the case that we could see that those which came directly from the Prime Minister's office were any more successful than those which came from a local member direct to the minister's office rather than through the Prime Minister's office,"Mr Boyd said.
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All of those representations from the Prime Minister's office were about projects in Coalition target seats,he added.
Mr Boyd said they could not see a"clear cause"for the funding of each project because there were 28 different versions of a colour-coded spreadsheet used in Senator McKenzie's office to decide recipients.
"So it's not the assessment against the published merit criteria using the published assessment process that determines success or failure,"he said.
Nor was it the advice of a backbencher,he added.
Mr Boyd said changes were made to the spreadsheet to move projects from approval to rejection,sometimes within hours,with no explanation as to why their status changed.
Sometimes a project backed by a Coalition MP would be slated for approval but later rejected,and sometimes the reverse would occur.
"The one thing we can say is there wasn't a record made as to why was this application funded and this application not funded,"Mr Boyd told the hearing.
When the audit officials asked ministerial advisers about these decisions,the responses included"couldn't recall"and"no record made at the time".