The group’s chief executive, Blair Jenkins, declared that his campaign was “under attack” from “forces unknown” as he confirmed the group had shut off its computer network following signs that e-mails were still being accessed illegally.
The move comes a week after the organisation says it first became aware that private information about its dealings might have been hacked into.
The group acknowledged earlier this week that a private e-mail, which is said had been unlawfully accessed, showed it had paid an academic £100 for writing a newspaper article which set out the case for a Scottish constitution.
The organisation came under fire for paying for the article by Dr Elliot Bulmer, of the Constitution Commission, a charity, which was published in the Herald newspaper with no indication it had been funded by the Yes Scotland campaign.
The pro-Union campaign Better Together wrote to Scotland’s charities regulator yesterday, urging it to mount an investigation into what it described as the “lack of transparency” over the payment.
Dr Bulmer insisted last night the payment was simply “compensation” for his time and was not a “bung” to ensure he wrote what Yes Scotland wanted.
A spokesman for Yes Scotland also said that no other payments had been made to third-party figures who it has commissioned to write for newspapers, including The Scotsman.
The group also dismissed claims by pro-Union figures that the hacking allegations were a “smokescreen” thrown up by Yes Scotland, in order to distract from questions about its payment to Dr Bulmer.
It is understood that officers from Police Scotland’s Digital Forensic Unit visited Yes Scotland’s offices again yesterday. Preliminary investigations could go on for “weeks”.
Mr Jenkins said last night: “The issue here is that the campaign for an independent Scotland is under attack from a force or forces unknown, clearly intent on causing as much disruption and damage to Yes Scotland and the movement as possible.”
He added: “As a result of this sustained criminal and sinister activity, Yes Scotland has been forced to shut down our entire internal online resource pending a comprehensive security audit of all our electronic systems. Make no mistake, what this amounts to is an attack on democracy.”
Figures in the group say they expect more private information has been hacked into, potentially including details of its communications strategy. However, it is not thought likely that sensitive information showing the names of individual donors could have been accessed.
And although reports suggested yesterday that the alleged hacker used a foreign IP address, it is understood that this does not rule out the computer being based in the UK.
The police were called in after a media inquiry last week about the payment given to Dr Bulmer – a payment which, sources say, was only known to a small group of people within the organisation. The ethics of that payment have been questioned by opponents.
A spokesman for Yes Scotland confirmed that it was “suggested” to Dr Bulmer that he write the article. The spokesman said: “At his request, he was paid a nominal fee for the considerable time and effort he spent on it. We had no input to, or any influence over, what he wrote.”
In the article Dr Bulmer said an independent Scotland offered “the chance to do things differently”, and described the SNP as a “pioneer” in showing how a new constitution could be written. There was no indication given that he had been paid for the piece by one of the two campaigns in the referendum campaign, nor that he was writing in a private capacity.
Mr Jenkins tweeted that it was “a brilliant must-read”, adding yesterday that the payment was “perfectly legitimate”.
Dr Bulmer said: “I did suggest that a small payment be made, not to buy my services of writing it, but simply as compensation for my time.
“I was paid £100 which is well below, I am sure people are aware, of the market rate for this kind of work and if I hadn’t accepted that sort of fee then questions could have been asked on the other side as to whether I was giving preferential treatment by giving them free work.
“It was a small fee for compensation for my time and certainly not the bung that it has been described by some.”
However, Better Together chief executive Blair MacDougall, said the campaign had sought to “deceive” readers.
He said: “What other supposedly independent voices are being paid bungs to say what the nationalists want? What else are they willing to do to deceive the people of Scotland?”
In a letter to the Office of the Scottish Charities Regulator (OSCR), he urged a full investigation into the issue.
An OSCR spokesperson said last night: “No decision has yet been taken whether to open an inquiry.”