The SNP stands to lose more than £1 million in public funding and could be forced to cut staff if it fails to appoint new auditors by the end of next month.
Stephen Flynn, the party's leader at Westminster, offered the bleak assessment today as police continue to investigate the Nationalists' finances.
It was revealed earlier this month the accounting firm the SNP relied on for 10 years had ended its business relationship last year - but many senior parliamentarians were not told at the time.
Flynn also claimed he only became aware of the lack of auditors on February 10 despite becoming the group’s leader in December.
If his party fails to appoint new auditors by May 31 it could lose around £1.2 million in Short money, the name given to the public funding provided to all opposition parties at Westminster.
Flynn, the MP for Aberdeen South, admitted to BBC Radio Scotland that such a scenario could see the party forced to cut jobs as a result.
"I thought it would be a relatively straightforward process to go and secure new auditors - that's obviously proven not to be the case," he said.
"Time has been an issue. We are now at the end of the financial year and everyone is seeking to do the same thing.
"Of course, we have additional pressures brought on by the fact there has been undoubted challenges with regards to the party in recent months."
Asked how the Westminster group could be impacted by the failure to appoint new auditors, Flynn added: "Very much the same space as the party.
"We are still trying to ensure we have an auditor in place in order to meet our deadlines - our deadlines are slightly different.
"We need to have our accounts for Short money in place by May 31. Every effort that can be made to ensure that happens is being made."
He continued: "I'm not going to make any commitments. It is a situation that is in a state of flux.
"I am very conscious of the fact that we have staff members who this relates directly to.
Asked if the SNP would miss out on Short money if it missed the deadline, Flynn said: "As I understand, that would be the case."
Short money is made available to all opposition parties in the House of Commons that secured either at least two seats or one seat and more than 150,000 votes at the previous general election.
The SNP as a whole is also currently lacking auditors, meaning the Electoral Commission could take action if accounts are not submitted on time.
It comes amid the ongoing police investigation into the SNP’s finances, which saw its former chief executive Peter Murrell and treasurer Colin Beattie arrested earlier this month.
Both men were released without charge pending further inquiry.
Flynn also said he became aware of the group’s lack of auditors on February 10, when a party official told him so.
It was put to him that his predecessor, Ian Blackford, had said that all “relevant information” was handed over to the new leader during the changeover in December.
Flynn added: “There may well have been discussions between other people but certainly, in relation to myself, I became fully aware of the situation on February 10.”
He said he did not receive the £33,000 salary boost which former Westminster leader Angus Robertson enjoyed.
Flynn said the salary top-up is “not something which I’m overly surprised about” given the additional responsibilities of the role.
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