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A constitutional expert was paid £100 by the pro-independence group Yes Scotland for a newspaper article he wrote.
The organisation has said that it had ``no input'' into the piece by Dr Elliot Bulmer and that he was the only person it had made such a payment to.
A Yes Scotland spokesman confirmed Dr Bulmer had been given £100, with this being done at the author's request.
The row over the payment came as police investigations continued into claims that Yes Scotland's email account had been hacked.
Blair McDougall, director of the Better Together campaign to keep Scotland in the UK, accused his rivals of ``secretly paying off supposedly impartial experts''.
The Tories also said that Yes Scotland had ``serious questions'' to answer.
In the article, which appeared in The Herald newspaper last month, Dr Bulmer was described as research director of the Constitutional Commission, with his piece titled ``'a Scottish constitution to serve the common weal''.
In it, he argued that independence offered Scotland ``the chance to do things differently'', adding that the ``best case for independence'' rested upon ``the belief that a Scottish state could do a better job of serving the common weal than the UK has done''.
A Yes Scotland spokesman said the organisation had confirmed last week that ``a small fee had been paid to Dr Bulmer at his request'', adding: ``We were perfectly relaxed and transparent about this.''
He added: ``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.''
A Police Scotland spokeswoman said: ``We can confirm a complaint has been made by Yes Scotland regarding unauthorised access to an email account.''
First Minister Alex Salmond has already described the hacking allegations as a ``very serious matter indeed''.
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.''