That announcement came after a conversation with Mr Cameron, who told the Andrew Marr Show: "This was one of the most serious cases we have had. It was technically within the rules but I have said that's not enough.
"It has to be a reasonable judgment and this was not a reasonable judgment and he has paid the price for that."
But with a petition being collected against Ms Kirkbride in her constituency, Mr Cameron gave her qualified support.
He said: "To be fair to Julie she does genuinely live in London, that's where her son goes to school, that's her main home and she does genuinely have a home in her constituency on which she claims a second home allowance.
"So I do think we have to look at that case separately. Obviously there are some questions raised in the papers today about other people living in the house and she'll have to answer those questions. But I do think the two cases are different."
The newspaper says Ms Kirkbride has been claiming over £1,000 a month in mortgage payments on the apartment in Bromsgrove, Worcestershire - plus thousands of pounds for maintenance.
But in a statement, she said: "My brother, Ian, stays in my Bromsgrove apartment and in my London home from time to time to help look after my son.
"I claim no expenses for my brother and neither do I pay him or claim for his help. He also acts as a volunteer in helping me with my office work and administration.
"Up and down the country families have their relatives stay with them and get them to help with things like childcare.
"Ian has his own home but prefers to stay with me and help me.
"There is no cost to the taxpayer in the arrangement and there is nothing for me to apologise for.
"To describe this arrangement as my brother living rent-free is a total distortion."
A petition has already been set up in Ms Kirkbride's constituency calling for her resignation.
Organisers of the Julie Must Go campaign say they hope to collect 10,000 signatures by the beginning of June.
Mr MacKay, who announced earlier he would leave Parliament at the next general election, claimed the second homes allowance on the couple's London flat which Ms Kirkbride declared as her main residence.
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