A council leader - now a Conservative MP - was warned his authority's money may have been misused two months before winning a seat in the General Election.
But Northampton Borough Council says it can find no record whistleblower concerns were passed on to them by David Mackintosh.
The MP says this is "incorrect" and the printed emails were "immediately passed to senior officers".
He added: "The officers were also aware of these emails."
Mr Mackintosh said the emails "had been published on an internet blog at the same time resulting in press queries to the borough council".
Months earlier, Mr Mackintosh's election campaign had received what later turned out to be a disguised donation of £30,000.
It came from developer Howard Grossman, accused in court papers of misappropriating millions of pounds of the council loan. The claim was settled out of court and the parties signed a non-disclosure agreement.
Millions of pounds out of £10.25m given to Northampton Town Football Club to redevelop its stadium is missing and the subject of a police investigation for "alleged financial irregularities".
On 18 February 2015, architect Stuart Loxton, using an alias, emailed his concerns to Mr Mackintosh and former council leader David Palethorpe.
A week later, on 25 February, he also sent Mr Mackintosh, now the Conservative MP for Northampton South, invoices detailing how some of the money may have funded unconnected schemes.
A council spokesman said: "We cannot at this stage find any emails or forwarded emails from Mr Mackintosh to council officers regarding the whistleblower and can find no record of any officers being alerted by Mr Mackintosh.
"In April 2015, the borough council's chief executive was made aware of the whistleblower by another person".
That "other person" was the then Labour councillor David Palethorpe.
Mr Palethorpe says he was surprised it fell to him to initiate a meeting between Mr Loxton and the council: "There are really serious questions which need to be answered."
The council says it was only after David Palethorpe had emailed them the whistleblower's details on 1 April that officers discussed the issue with Mr Mackintosh.
Mr Loxton had been commissioned by Mr Grossman and his associates to draw up a string of planning applications in Hertfordshire in 2014.
He was instructed to entitle the invoices 'Northampton Football Club' and send them to Mr Grossman's company, 1st Land Ltd.
The firm was set up for the purposes of redeveloping Sixfields stadium and received more than £7m of the council loan money.
Work was halted on the stadium when contractors were not paid by 1st Land.
Mr Mackintosh was elected MP for Northampton South in May last year, having received £30,000 in three donations to his campaign fund in April and May 2014.
A BBC investigation has established this money did not originate from the individuals declared to the Electoral Commission but from Mr Grossman's company 1st Land Ltd.
One of them, Leonard Western, subsequently said he was unaware of the payment made in his name and told the BBC he was a Labour supporter.
The Electoral Commission was handed the BBC's evidence back in April but has yet to respond.
Mr Grossman has denied any loan money was misappropriated. He has described the allegations in court papers as "outrageous and deeply offensive".
In a statement, the Northampton Borough Council said: "The whistleblower was asked to provide evidence of his claims.
"We also asked him to report the allegations of criminal activity to Northamptonshire Police.
"He did provide us with copies of invoices subsequently, but they did not show any direct misuse of council loan monies. All of this information was kept on file.
"When further concerns then began to emerge, we made the police aware of the whistleblower's allegations and the information began to fit in to our wider picture of what has happened, which is now being investigated both by auditors and by Northamptonshire Police".
Mr Mackintosh told the BBC he welcomed the police investigation currently taking place.
"All legal responsibility for the negotiation and background security checks relating to the loan rested with senior officers of the council. No elected members were directly involved in this," he said.
"During the General Election, the allegations were, and remain, unproven and were still being investigated, but I did convey my concerns about Sixfields whenever I was asked."
'I have repeatedly told the BBC, all donations were made to, and processed by, Northampton South Conservative Association. No donations were made to me personally."