Nicola Sturgeon said the SNP did not lie to journalists about the number of members who had left the party in recent years.
The outgoing First Minister said the party had "mishandled" the situation and claimed "the SNP's not in a mess".
Sturgeon's husband and party chief executive Peter Murrell resigned from his role on Saturday amid reports that he was facing a vote of no confidence from party members.
SNP head of media Murray Foote stood down just hours before in response to the publication of the membership numbers.
The party was finally forced to admit last week that it had lost 30,000 members over the last two years - despite rubbishing earlier reports of an exodus.
Acting CEO and party president Mike Russell said the party was in a "tremendous mess" and that he had "no idea" why journalists had been misled over the membership numbers.
But Sturgeon denied that the party was in a mess.
She told ITV's Loose Women on Monday afternoon: "Mike [Russell...] was referring to some of the issues around the leadership election.
"The SNP's not in a mess. It's going through... some growing pains. They are necessary but they're difficult."
She also denied the party had intentionally misled journalists over how many people had left the party.
She said: "My husband has been chief executive of the SNP for longer than I have been leader. He was going to step down... and has decided to teak responsibility for that situation, I think rightly.
"But we were asked a specific [question]... we mishandled that situation.
"When asked a specific question, not 'What's the size of your membership?' but 'Have you lost 30,000 members because of x and y?'
"In that sense, we should have framed it in a bigger way.
"So these things are all an opportunity to learn and to reflect."
Tory MSP Meghan Gallacher said: “It’s clear Nicola Sturgeon has already mentally checked out of Bute House and is focusing on the next phase of her life.
“But as she heads off into the sunset, the First Minister – along with her husband – leave a trail of destruction in their wake for the SNP and the country.
“How she can deny her party is in a mess is mind-boggling, given her departure has sparked a brutal civil war.
“The leadership contest has seen her record in government trashed by all of the feuding candidates, two of whom have questioned the integrity of the contest itself, while her chief executive spouse and the SNP’s media chief have both been forced to quit over lies told about membership figures."
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