Ms Dorries, who represents Mid Bedfordshire, faces an inquiry into her spending on accommodation and travel.
In a statement, IPSA said it had reason to believe she had received expenses “that should not have been allowed”.
But the MP, who was suspended from the Conservatives in November, said there was “no foundation” to the claims.
The withdrawal of the party whip from Ms Dorries followed her decision to take part in the ITV show I’m a Celebrity, Get Me Out of Here.
Ms Dorries, a former nurse who has been an MP since 2005, is currently sitting as an independent.
She told the BBC she believed the inquiry had been triggered by her accommodation costs for the apartment she rents in Westminster.
In May, June and July last year, her claims were slightly higher than usual, she said, because her daughter was staying with her.
She also said it may have been prompted by a mistake by her parliamentary assistant, who accidentally claimed twice for petrol costs.
The MP said: “I have never claimed a penny in my expenses that I shouldn’t have claimed. There is absolutely no foundation to this investigation by IPSA. They suspect that I sublet my flat for three months. I certainly didn’t.
“Any MP that went through the MP’s expenses scandal would have to be mad to have sublet any property since.”
A spokesman for IPSA confirmed the focus was on claims made in 2011 and 2012, but declined to comment further.
“The Compliance Officer for the Independent Parliamentary Standards Authority has reason to believe that Ms Nadine Dorries MP may have been paid an amount under the MPs’ Scheme of Business Costs and Expenses that should not have been allowed,” a statement on IPSA’s website said.
“In accordance with the legislation and the procedures for investigation made thereunder, no further information shall be published until the investigation has been concluded.”
Ms Dorries met Conservative chief whip Sir George Young having returned from Australia in November last year, to explain why she had taken time off to be on the reality TV show I’m a Celebrity.
Afterwards, a spokesman for Sir George said: “The whip has not been restored and nor will it be until she proves that she can rebuild bridges with her
constituents, her association and her parliamentary colleagues.”
In April 2012, Ms Dorries described David Cameron and George Osborne as “two arrogant posh boys” with “no passion to want to understand the lives of others”.
Nadine Dorries is an outspoken MP keen on being in the public eye, even more than most.
Last year, she defended her appearance on I’m a Celebrity in Australia as a “publicity gift.” She was voted off first.
An investigation into her expenses is a development she won’t relish. Nothing which reminds voters of Westminster’s expenses scandal can be good publicity for an MP, particularly an independent one.
The Mid Bedfordshire MP is not showing it though. She’s already threatening legal action and is vigorously defending any suggestion the received a penny more than she’s entitled to.
Ms Dorries insists that she never sublet her apartment – and in her own words: “I might be called mad Nad; I’m not that mad.”
Her chances of winning back the Conservative whip any time soon may have receded.