Mr Coburn, an MEP and UKIP’s only elected politician in Scotland, failed to win enough votes to win a place on the Highlands and Islands regional list.
The party failed to deliver one MSP, despite standing a total of 26 candidates across eight regions.
In an email to party activists, the Scottish UKIP leader accused others within the party for the defeat - a claim denied by other members who fear Mr Coburn’s views will ultimately bring about an end of UKIP in Scotland.
He said in the email: “We were let down by a tiny group of dreadful careerists putting themselves above the party’s interests. They will be dealt with.”
A party spokesman said Mr Coburn was indicating that disciplinary procedures will be used “to rid the party of anyone that deliberately set out to cause the party harm during the campaign”.
However, Robert Malyn, a former aide to Coburn and a candidate on UKIP’s West of Scotland regional list, said: “This email is announcement of another Stalinist-style purge of his critics and presumably anyone who does not toe the party line. It will see the end of UKIP in Scotland.
“Mr Coburn is a lame duck leader for the next three years. If we vote for a Brexit he’ll be gone by 2018 and if we don’t it’s likely that the Greens will take his seat, unless UKIP members in Scotland get the chance to deselect him and replace him with someone more credible.
“Basically UKIP is no longer fit for purpose and for that reason many have now left the party.”
Meanwhile, Euan Blockley, who quit UKIP for the Scottish Conservatives weeks before the Holyrood election, said: “When I was a UKIP member I had only the party’s best interests at heart.
“Credible candidates were then betrayed by a UKIP top brass that is completely disconnected from the party membership.
“The fact David Coburn is claiming that I and others are self-serving sounds like hypocrisy and is laughable.”
Also in the email, Me Coburn claimed the Scottish media had “done their best to ignore or trash us” and condemned “disgraceful” television stations for failing to offer the fringe party more airtime.
Mr Coburn also suggested that he intentionally made glaring policy errors in public to draw attention to the party.
He wrote: “By being controversial and colourful I have been told by the press I managed to get as much publicity as Sturgeon to the annoyance of the other party leaders.
“One man’s deliberate ‘gaffe’ is another man’s publicity opportunity.”
A party spokesman suggested leader Nigel Farage backed the tactic.
UKIP polled around two per cent of the vote in each area, meaning the party lost eight £500 deposits.
There are 1,000 UKIP members in Scotland, according to the party, but insiders claim that figure may now have dropped to around 600.
• An earlier version of this article carried an incorrect headline which has now been rectified.