THE MP at the centre of a £30,000 police probe into Women for Independence only paid the group £6,000 after months of facing questions about its accounts, it has emerged.
Key figures in the campaign group are understood to have pressed the Glasgow East MP for details of the group's income and expenditure since the summer.
However, Ms McGarry repeatedly failed to account for alleged financial discrepancies at the organisation and only paid the group around £6,000 when she was earning a salary as an MP.
McGarry, 34, who co-founded Women For Independence in 2012 and was in charge of its finances until the spring, resigned the SNP whip on Tuesday, 48 hours after the group's executive told the police around £30,000 was apparently missing from its funds.
The MP, who denies any wrongdoing, controlled a Women For Independence PayPal account which received more than £51,000 in donations raised through online crowdfunding appeals. The account was linked to her own bank account.
It had spent around £26,000 in support of a yes vote in the referendum.
One senior SNP source said there had been concerns about the pro-independence group throughout last year.
“She [McGarry] was in charge of the PayPal stuff and the organisation and paying money out. “It was chaotic. She couldn’t keep on top of it. But the buck stops with her. At the end of the day, she took all the credit and all the kudos and WFI came out smelling of roses.”
The SNP was last night accused of double-standards after repeatedly refusing to disclose when the First Minister Nicola Sturgeon first knew of financial allegations involving Ms McGarry.
Ms Sturgeon’s special advisers said it was a matter for the party, not the government.
However the party then repeatedly refused to say what the SNP leader knew and when.
This was in spite of Ms Sturgeon stating publicly when she became aware of the property scandal around Edinburgh West MP Michelle Thomson, who quit the SNP whip in September.
Like McGarry, Ms Thomson was elected in May in the SNP's landslide election victory in Scotland.
On September 30, Ms Sturgeon said the first she had read about Ms Thomson's alleged property dealings was in a newspaper.
It then published its first stories on Thomson’s £1.7m property empire on September 20.
It is understood the seven SNP Holyrood candidates on the WFI executive were also warned by the party last week not to talk to the media about what they know.
A Labour spokesman said: “The SNP need to realise how serious this is.
There are clear links between senior members of WFI and the highest officials in the SNP - they need to disclose who knew what when as soon as possible.
"In the Michelle Thomson case Nicola Sturgeon was clear when the SNP first learned of her business deals, the same standard should be expected in this case."
A source close to the MP said of the £6,000 payment: "That was part of the process of things being tidied up. Money was lying around in the account dormant. If someone was accused of doing a runner, money would not be dormant in an account."
According to reports, other friends of the MP said she "misjudged" the seriousness of the dispute over the missing funds and feels "betrayed" her Women for Independence colleagues called in police.
One was quoted as saying: "Natalie accepts that with immense pressure of work she failed to prioritise WFI but there was nothing sinister about that.
"She clearly misjudged the situation.
"She is guilty at most of burying her head in the sand. It really is said it has come to this but many of us feel betrayed by senior figures at WFI who jumped the gun before giving Natalie any real deadline to get the paperwork in."
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