Yes Scotland, headed by Blair Jenkins, filed a police complaint after private emails were allegedly accessed. It became aware after it received a media inquiry last week that appeared to contain information from internal correspondence.
The details of the email in question were not initially released but Yes Scotland has now revealed it was a correspondence with Dr Elliot Bulmer in connection with an article he wrote for The Herald in July, A Scottish constitution to serve the common weal.
The pro-independence group said it had no influence over what he wrote and revealed the details of the email to end "unhelpful speculation". It is understood Yes Scotland paid Dr Bulmer around £100 for the article.
The Herald has made clear that it was offered the article and accepted it in good faith; made no payment to Dr Bulmer; and readers were in no doubt about the author's background.
Today, as the issue became one of the most controversial of the refernedum campaign to date, Yes Scotland said it had closed down part of its computer system as experts carried out what Mr Jenkins described as a "comprehensive security audit" as a result of "sustained criminal and sinister activity".
Their campaign opponents, Better Together, accused Yes Scotland of ''secretly paying off supposedly impartial experts'' and director Blair McDougall has also asked the Charity Regulator to carry out an urgent inquiry into the payment since Dr Bulmer is research director of the Constitutional Commission, a registered charity which states that it has no political aligment.
Mr McDougall claims that, since Dr Bulmer did not appear to be writing as a private citizen, and the commission tweeted a link to the Herald article, "it appears that a political campaign has made payment to an employee of a registered charity in return for an article which was published in the name of that charity".
A Yes Scotland spokesman said: "This matter was first brought to our attention last Wednesday when we were asked for comment on Dr Bulmer and the article in question. We responded quickly, confirming that a small fee had been paid to Dr Bulmer at his request. We were perfectly relaxed and transparent about this.
"However, later that day it became apparent that an email account at Yes Scotland had been accessed illegally and that the information relating to this matter had been gleaned as a result.
"We alerted the police and British Telecom as well as the enquirer who, upon reflection, decided to not proceed further.
"Given that the illegal breach of Yes Scotland email has become the subject of an extensive and ongoing police inquiry involving detectives from Police Scotland's Digital Forensics Unit, we have - under legal advice and at the request of the investigating officers - been unable to discuss the content of the email relating to Dr Bulmer.
"However, given persistent unhelpful speculation, we can confirm that in the course of a wide-ranging discussion with Dr Bulmer it was suggested that he, as an academic working in a private capacity, might consider writing an article on matters about constitutional frameworks based on his expertise.
"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.
"We would now ask that this serious criminal investigation is allowed to continue unhindered by further unhelpful speculation, accusation and misinformation."
Today, Mr Jenkins added: "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.
"This criminal activity, which is the subject of a major police investigation, is intense and ongoing.
"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."
He said: "Make no mistake, what this amounts to is an attack on democracy."
He said the "very serious and malicious disruption" Yes Scotland had suffered had increased the group's determination to campaign for a Yes vote in next September's independence referendum.
Mr Jenkins said: "The people of Scotland deserve much better. For our part, this very serious and malicious disruption has simply doubled our determination to go on making the positive and optimistic case for an independent Scotland and to win a decisive victory on September 18 next year."
Mr McDougall said: "If there has been any illegal activity, then we hope that the police are able to track down the culprits."
But he added: "These allegations against Yes Scotland, if true, fatally undermine trust in the independence campaign. How can we believe what they say if they are secretly paying off supposedly impartial experts?
"The leadership of Yes Scotland must take responsibility for this and answer these accusations. Who else received payment? Who knew that this kind of payment was being authorised by the campaign's chief executive? 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?"
A Scottish Conservative spokesman said: "With the people of Scotland facing the biggest decision in 300 years they deserve to have independent analysis that is actually independent.
"Clearly, Yes Scotland now have some serious questions to answer in relation to this matter."
Former Liberal Democrat leader Sir Menzies Campbell said the payment "not only reflects badly on Yes Scotland, it undermines the transparent and open debate of the issues around independence that Scotland needs".
Sir Menzies argued: "Ultimately, this has called the integrity of the Yes Scotland campaign into question.
"It is important that any hacking allegations are investigated fully but we cannot ignore the content of the messages that were leaked.
"This is about transparency and it is about honesty. There are real questions that Yes Scotland need to answer over why they felt it was appropriate for them to make this payment.
"The simple fact is that when writers are producing work on behalf of a campaign group, their readers need to know about it."
A spokesman for the Herald & Times Group said: "We were offered an article for our opinion pages by a constitutional expert, which we accepted in good faith as a valid contribution to the referendum debate.
"We declined a request for payment and the author's background was made clear to our readers."