While the SNP hope the job losses can all be done through a voluntary redundancy scheme, a senior source told media that compulsory redundancies could also be made.
The party has seen income fall in recent years, with major donors all but drying up, in part because of Operation Branchform, the ongoing police investigation into missing funds.
The most recent accounts show that membership has also plummeted, and is now around 64,000, almost half its 2019 peak of 126,000 members.
They have also lost around £900,000 in Short money, the public cash given to all opposition parties in the Commons with two or more MPs.
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Speaking to BBC Scotland’s Sunday Show, Mr Flynn said: “It’s a tough but necessary decision, as I understand it, to make sure that the party’s in the best condition possible going into the 2026 elections.
“Obviously, earlier this year, I had to go through a very similar process with SNP staff down in London.
“It’s an incredibly tough and challenging experience to go through. My thoughts are all very much with all of the HQ staff, who I know very well, who will be having a very troubled weekend.
“And I think when we’re having the wider discussion in relation to this, we need to be mindful of the fact that there are people behind these numbers, people with friends and families and responsibilities.
“And hopefully this can all be done in a way which is hopefully as swift as possible to ensure that we get in a position where the party is able to fight the election, but hopefully meet the needs of those people.”
Mr Flynn said the key to the party having a big staff staffing group, “is making sure that you’re in a position to to attract investment.”
“That’s the same for all our organisations,” he added. “I would like to think that I can maybe play a role in the future in helping to make sure that the party is able to attract further investment into the organisation, and I’m sure that applies to all, to all elected members.”
News of the redundancies comes just weeks after Murray Foote unexpectedly quit as chief executive.
He said he could not make the “necessary personal commitment” to lead the “substantial process of internal re-organisation and renewal” needed to prepare for the 2026 election.
Carol Beattie, the former chief executive of Stirling Council, is currently serving as the interim chief executive.
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Announcing the redundancies on Saturday, the SNP said staffing costs currently account for 81% of income from membership fees compared to 2015, when it was 35%.
Alex Kerr, the party’s national secretary, said: “The NEC has been tasked with delivering a modern, dynamic election-winning party to win in 2026 and beyond and today’s agreement to consult on a new structure at headquarters makes key progress to deliver on that aim.
“The proposal agreed by the NEC today would get HQ into shape for future elections and for the fight for independence.
“It would mean that not everyone currently employed at HQ will continue with us but a streamlined headquarters protects the long-term finances of the party and delivers on the modern, professional, election-winning organisation Scotland needs.”