Humza Yousaf has said the former SNP chief executive Peter Murrell will not be suspended from the party because he is “innocent until proven guilty”.
But the SNP leader confirmed the party would not be paying Mr Murrell’s legal fees.
Mr Murrell, who is Nicola Sturgeon’s husband, was arrested last week amid a police probe into the SNP’s finances but was released without charge.
Mr Yousaf also confirmed the party’s auditors resigned six months ago.
The BBC revealed last week that the SNP’s accountants Johnston Carmichael, who had worked with the party for more than a decade, had resigned.
The SNP has told the Electoral Commission it is having difficulty identifying a replacement.
During an event in Leith, Mr Yousaf faced questions from reporters about when exactly they had quit, and what he had known about it.
Mr Yousaf said the auditors had resigned “round about October of last year” but he only found out when he became first minister.
It was later clarified that Johnston Carmichael told the party in September that it would not be able to conduct the audit due in 2023.
He was also pressed on whether Mr Murrell, 58, should have his membership suspended while the police investigation was continuing.
The first minister said while it was “undoubtedly serious” that the former chief executive had been interviewed under caution, he did not think he should be suspended from the party.
“I tend to work on the premise that somebody is innocent until proven guilty,” Mr Yousaf stated.
In response SNP MP Joanna Cherry wrote on Twitter: “Of course Murrell is innocent until proven guilty but the decision not to suspend his party membership given the whole circumstances is remarkable.”
The party’s interim chief executive Michael Russell has described recent developments as the biggest crisis for the SNP in 50 years.
Mr Yousaf acknowledged that it was a “difficult” period for his party.
“It has got the potential to damage the party, we know that,” he said.
But he insisted the SNP was still in a “position of strength” as the largest political party in Scotland and there was an “opportunity to rebuild”.
Mr Yousaf insisted that appointing new auditors was currently one of the “major priorities” for the party
He said he hoped to have the accounts prepared in time to be submitted to watchdogs at the Electoral Commission in July, although he accepted this was “problematic”.
“We’re going to try to work to the premise that we can get them ready by July. It will be a challenging task,” he said.
It is understood that the SNP has approached a number of firms about auditing their accounts but have not yet found one with the capacity to take them on.
A spokesperson for the party said: “We have informed the Electoral Commission of the difficulty in identifying replacement auditors and the national treasurer has made the party’s finance and audit committee aware.”
In July 2021 Police Scotland launched a formal investigation into the SNP’s finances after receiving complaints about how donations made for a fresh independence campaign had been used.
Nearly £667,000 is believed to have been raised through referendum-related appeals, but questions were raised after accounts showed the SNP had just under £97,000 in the bank at the end of 2019, and total net assets of about £272,000.
Last year it emerged Mr Murrell gave a loan of more than £100,000 to the SNP to help it out with a “cash flow” issue after the last election.
Mr Murrell resigned as SNP chief executive last month after taking responsibility for misleading statements about a fall in party membership.
The number of members had fallen from the 104,000 it had two years ago to just over 72,000.
Scottish Conservative chairman Craig Hoy called for the SNP to “give a full account of what has been going on in the management of their party”.
“It is an extraordinary revelation that the SNP’s auditors resigned as far back as October, when senior figures have spent months maintaining that there were no questions over the party’s finances,” he said.
Meanwhile Scottish Labour’s deputy leader Jackie Baillie raised concerns that the SNP “did not come clean” about losing their auditors for several months.
“It is deeply worrying if they have been unable to replace the auditors in all this time,” she said in a post on Twitter. “It is time for the secrecy to end.”