The crowdfunded money was donated to the SNP by supporters to help fund the next referendum campaign, only for many independence activists to allege this money has ‘disappeared’ from the SNP accounts.
Police are now reportedly investigating 12 new fraud complaints over the funds as part of their probe into the missing donations.
It will increase pressure on First Minister Nicola Sturgeon’s husband Peter Murrell, who is the party’s chief executive.
It is now believed senior party figures including Mr Murrell will be interviewed by police, with The Mail on Sunday claiming they will also seek warrants to get access to documents.
A source told the newspaper: “Around a dozen more allegations have emerged since police announced their investigation.
“Those people have to be seen, to give formal statements, and that will slow things down a bit.
“But once that is out of the way, police will seek warrants to examine the documents the auditors would not give up voluntarily, and they’re also expecting to seek a warrant to get the party’s lawyers to hand over relevant documentation.
"After that, it is a certainty that they will want to question the party’s accountants and senior office bearers, in particular the treasurer and the chief executive, and possibly the lawyers as well, depending on what they discover.
"It is not yet guaranteed that any of these people will be interviewed as suspects.
“That will depend on what they learn from the statements being taken over the coming days and the documents they expect to recover through warrants.”
The SNP said it would co-operate fully with the investigation.
Another senior figure claimed the missing money was Mr Murrell’s responsibility.
They said: "This money has become a bit like the emperor’s new clothes.
"We knew it wasn’t there, but people kept insisting it was, even though we couldn’t see it.
"Now the police are investigating. That has really brought it home.
"These financial issues have not been handled in a positive way. No matter what happens now, the fact that police are having to investigate shows that he is probably not the right man for the job.”
The funding controversy led to the party’s former treasurer, Douglas Chapman MP, and high-profile MP Joanna Cherry stepping down from their positions on the party’s national executive committee earlier this year due to concerns around transparency.
Opposition parties have now claimed the scandal is damaging trust in Scottish politics.
Scottish Conservative chief whip Stephen Kerr said: “Nationalists are clearly furious that their money has vanished into an SNP murky black hole.
"It’s right that Police Scotland are investigating whatever happened here because it’s clear the SNP won’t come clean.
"They are dragging down Scottish politics with this affair.”
Liberal Democrat MP Wendy Chamberlain said: ‘They [the SNP] seem to be no better at handling supporters’ money than they are handling that of Scottish taxpayers.”
An SNP spokesperson said: “We will co-operate fully with the police investigation and will make no further comment.”