Peter Adams has resigned as Ukip's regional organiser citing a "breakdown" in his "working relationship" with the party chairman.
The SNP described Ukip as a "farce" and said the party would continue to be "rejected" by voters.
The anti-EU party, led by Farage at a UK level, has been tipped to win May's European Parliament election. Party members are hopeful that they can return an MEP north of the Border. But divisions inside the Scottish party are threatening to undermine its prospects.
Last year, the then Ukip Scotland leader Lord Monckton and his allies believed three members based in Edinburgh were planning a takeover of the party.
The row spilled over into the internal election to rank candidates for the European poll, with six of the nine shortlisted - including Monckton - quitting in protest.
Mike Scott-Hayward and Malcolm Macaskill then quit as Scottish chair and chief fundraiser respectively, while Farage sacked Monckton from his leadership post.
Monckton blasted Farage and claimed the Scottish party had been "wiped out".
Adams, who was tasked with making Ukip an election-winning force, has now also walked away.
In an email to members, he pointed the finger at UK party chair Steve Crowther: "Contrary to some rumours being spread around I have no health problems and am not leaving Ukip, and to dispel other rumours, the main reason for me standing down is due to the breakdown in the working relationship between myself and the party chairman.
"It is disappointing that the egos of three of our Edinburgh members has lead [sic] to so much disruption over the past nine months and spoiled our build up to the European elections. Remember the old adage 'As you sow, so shall you reap'."
Adams is a party stalwart who polled 0.4% in the Livingston by-election in 2005, 1.7% in the Kirkcaldy and Cowdenbeath constituency at the last General Election, and 3.75% at last year's Holyrood by-election in Dunfermline.
David Coburn is the party's "lead candidate" in Scotland for the European election. Right-winger Misty Thackeray is interim Scottish chair.
An SNP spokesperson said: "Ukip are a total farce and barely exist as a party in Scotland."
Adams said: "I stood down as regional organiser at the end of December."
A Ukip spokesman said: "Peter was a well-liked and hardworking member of Ukip. We want to thank him for his years of service and wish him all the best in the future."