An SNP MP’s bank account is at the centre of the row over nearly £30,000 that has allegedly gone missing from a pro-independence campaign group.

Donations raised by Women for Independence (WfI) were made through an online PayPal system linked to Natalie McGarry’s own account.

McGarry withdrew from the SNP whip yesterday after police launched an investigation into a complaint by the equalities organisation.

WfI, one of the most high-profile Yes groups, announced on Sunday that it had called in the police over alleged discrepancies between its income and expenditure.

The police referral followed an internal audit carried out by two senior WfI figures and a chartered accountant covering 2014 to March this year.

McGarry, who was elected in May to serve Glasgow East, was responsible for finance and is at the heart of the row.

However, the MP's solicitor has said she denies any wrongdoing.

According to WfI sources, the campaign group had two separate accounts during the period that is under the spotlight.

The first was a WfI bank account that was largely cheque-based.

The second was a PayPal account used to collect online donations for WfI activities, including campaigning.

WfI had three online crowd-funders in 2014, raising £20,823 in April, £15,186 in August and £15,615 in October.

Potential donors were promised the group would use “every penny wisely”.

The audit revealed concerns about money raised through the PayPal system linked to McGarry’s own account.

A new PayPal account, unconnected to McGarry, has since been set up.

According to the WfI financial report from March 2015, which is in the MP’s name, the group raised £49,816.23 in 2014 after deductions, spent £28,500 during the referendum short campaign and £8,700 prior to this period.

After the referendum, she stated that £2,500 was spent on wages, £2,900 on merchandise, £910 on postage and almost £3,800 in donations to food banks in Perth and on hall hires.

Around £4,000 was “carried down” into 2015 and £8,000 was in reserve.

McGarry noted: “The accounts will be fully audited and presented to the first available meeting of the new national council.”

However, the accounts have not been audited.

Twenty members of the group’s national committee, seven of whom are SNP Holyrood candidates, signed a statement claiming:

“We have identified an apparent discrepancy between our donation income and the expenditure which we currently have evidence of. We have exhausted all opportunities of obtaining adequate evidence or explanation to account for this discrepancy.”

McGarry played a key role in another pro-independence group, Yes Glasgow, that also used online fundraising to collect £5,465 in donations.

The money was intended for printing and distributing a minimum of 100,000 leaflets advertising the debate, venue hire, publicity and equipment.

Aamer Anwar, McGarry's solicitor, did not respond to a request for comment on the bank account issue.

However, in a general statement issued to media yesterday, he said: "Natalie McGarry MP has decided to withdraw from the party whip although she is fully aware that this will lead to automatic suspension from the SNP; She has taken this step in the best interests of the party and the constituents of the East End who voted for her.

"She maintains she has done nothing wrong but is conscious that the events of the last 48 hours are distracting from the job she was elected to do on behalf of the SNP. She has a proud record as a principled activist and states she is determined to clear her name.

"Fortunately in our legal system we still believe in a presumption of innocence. What has been reported to Police Scotland are financial discrepancies, yet they have not even established whether criminality is involved."