The SNP's chief executive, Peter Murrell has resigned from the role with immediate effect.
Reports had suggested members of the SNP's ruling National Executive Committee had threatened a vote of no confidence in Mr Murrell, who is married to the party's outgoing leader Nicola Sturgeon.
It follows the departure of the SNP media chief Murray Foote, who left yesterday amid a row over the party's membership numbers.
Mr Murrell has been the party's chief executive for more than 20 years.
In a statement, he said: "Responsibility for the SNP's responses to media queries about our membership number lies with me as chief executive.
"While there was no intent to mislead, I accept that this has been the outcome. I have therefore decided to confirm my intention to step down as chief executive with immediate effect.
"I had not planned to confirm this decision until after the leadership election.
"However, as my future has become a distraction from the campaign I have concluded that I should stand down now, so the party can focus fully on issues about Scotland's future.
"The election contest is being run by the national secretary and I have had no role in it at any point.
"I am very proud of what has been achieved in my time as chief executive and of the part I have played in securing the electoral success the party has enjoyed over almost two decades.
"Fourteen national election wins is testament to the skills of the dedicated and talented HQ team that I have been privileged to lead.
"They give their all to the party and the independence cause and I thank them for it.
"I have worked for independence all my life and will continue to do so, albeit in a different capacity, until it is achieved - and I do firmly believe that independence is now closer than ever."
Earlier this week, it emerged that the party had lost 30,000 members in just over a year.
Mr Foote said that after speaking to the party's HQ, he had issued responses to the media which had "serious issues" and he later decided there was a "serious impediment" to his role.
Ms Sturgeon announced on 15 February that she was stepping down as Scotland's first minister, triggering a leadership contest which is yet to conclude.
On Thursday, the party revealed membership as of 15 February was 72,186, having fallen from 103,884 in 2021.
This corroborated a story in the Sunday Mail in February around the SNP losing 30,000 members, something Mr Foote had strongly denied at the time.
The Herald newspaper has reported a senior member of the NEC said: "We have the numbers. There's not a hope in hell that Peter can survive a no confidence motion."
Earlier, SNP leadership candidate Kate Forbes had acknowledged "extraordinary turmoil" in the party.