The comments followed an NDP news release, in which the party claimed the probe was "in response" to their concerns about the Liberals' decision to bail out the MaRS innovation and research complex.
The deal in question was first brought to light last week, when the Progressive Conservatives released documents showing the Liberal government gave MaRS a $71-million grant to buy land and a $234-million loan for a new tower.
The Tories said documents showed the money couldn't be repaid and that the Liberals had agreed earlier this year to purchase the new building to house government offices.
According to the documents, the development's $317-million purchase price would include the $234-million loan.
Premier Kathleen Wynne has defended her government, saying the deal was not made public because it hasn't been finalized.
While the Tories led the charge in hammering Wynne for trying to cover up the full cost of the "bailout," NDP candidate Gilles Bisson wrote to auditor general Bonnie Lysyk, asking her to look into the Liberal government's "secret payment" involving MaRS.
"Ontarians deserve to know the full cost of the government's election-eve decision to bail out the MaRS building, and whether or not the government exercised due diligence in its negotiations, and whether the government has any financial justification for agreement," he wrote.
Lysyk wrote back to Bisson, saying her office was already looking at the MaRS deal.
"As it happens, we are currently conducting an audit of Infrastructure Ontario's Loans Program and the scope of that audit includes the loan made to facilitate completion of the MaRS phase 2 building," the letter said. "You raised a number of questions that we will consider in drafting the chapter covering this audit."
A spokeswoman for Lysyk told The Canadian Press the audit started last year as part of the "normal audit cycle."
"We're looking at everything in that loan program," said Christine Pedias, adding that the office's findings will be part of the auditor general's annual report.
NDP Leader Andrea Horwath appeared to backtrack on her party's claim that the audit was triggered by the NDP request.
"We have no way of knowing what the auditor general is or isn't doing," Horwath said in Niagara Falls.
"In this case we sent out the request. We had no idea whether she was or she wasn't (investigating). But all I'm saying is we are all on the same track. "
The Liberals lashed out at the NDP over the matter.
"Desperate and devoid of a positive progressive plan of their own, today Andrea Horwath attempted to revive her struggling campaign by deceiving reporters about a regular report being undertaken by the auditor general as part of her annual report," they said in a news release.
But Horwath laughed off the accusations, saying the NDP often asked the auditor general to look into various matters.
"The Liberals always have a spin for something. It seems to me that the most important piece here is that New Democrats are always on the job," she said.
"Liberals have wasted tax dollars, they've misused tax dollars and they have behaved in a way that is corrupt and inappropriate. Ontarians need to make a decision about what their future looks like."
Also on Thursday, Horwath promised that one of her first acts as premier would be to bring in legislation that would help Ontarians trust their government again.
New Democrats would do that by strengthening the ban on partisan government advertising and expanding the Ontario Ombudsman's oversight of health care, long-term care and the province's troubled Ornge air ambulance service, Horwath said.
"That will help us with cleaning up Queen's Park," she said. "New Democrats are determined, if we're given the opportunity, to work day in and day out to try and rebuild trust in government for the people of Ontario. This act is going to be an important step in that regard."
The "Respect for Ontarians Act" would be introduced within 30 days of the New Democrats forming government.