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In an interview with STV News, the SNP leader and Scotland’s First Minister rejected allegations that £600,000 of funds raised by activists has “gone missing”.
Joanna Cherry resigned from the National Executive Committee (NEC) of the party on Monday while Douglas Chapman quit as the SNP national treasurer on Saturday.
Ms Sturgeon said: “I’m not concerned about the party’s finances.
“The finances of the SNP are independently audited, our accounts are sent to the Electoral Commission in common with other parties and of course published so there’s full scrutiny around that.
“Money hasn’t gone missing. All money goes through the SNP accounts independently and fully audited.
“We don’t hold separate accounts, we’re under no legal requirement to do that, our accounts are managed on a cash-flow basis.
“But every penny we raise to support the campaign for independence will be spent on the campaign for independence.”
Edinburgh South West MP Ms Cherry blamed issues over “transparency and scrutiny” in the party.
In a statement on Twitter, she said: “I’ve resigned from the NEC of @theSNP.
“A number of factors have prevented me from fulfilling the mandate party members gave me to improve transparency & scrutiny & to uphold the party’s constitution.
“I won’t be making any further comment at this stage.”
Mr Chapman, MP for Dunfermline and West Fife, said he was not given enough information to do the job as treasurer.
He took over the role last year, while Ms Cherry only recently returned to politics after taking a break for health reasons.
It remains unclear what led to Mr Chapman’s decision, but SNP business convener and fellow MP Kirsten Oswald said she “fundamentally disagrees” with Mr Chapman’s assessment.