THE Electoral Commission is to examine claims that the SNP's chief executive broke spending rules in the run-up the referendum by helping to run a pro-independence campaign group which claims to be party-politically neutral.

A complaint has been made to the watchdog after leaked emails allegedly showed that Peter Murrell, who is married to Nicola Sturgeon, influenced the management of the Business for Scotland (BfS) organisation.

It will now look into allegations that the two groups were 'working together', which if proven would have implications over strict spending limits imposed on official campaigners.

The claims were dismissed as "nonsense" by the SNP, with a spokesman denying there had been joint working with BfS which was run by Michelle Thomson. Ms Thomson went on to become an SNP MP and resigned the party whip after allegations surrounding her property dealings surfaced.

Labour described the allegations as "hugely serious" with Jackie Baillie, the party's public services spokeswoman, saying: "If it is proven that these groups were established and effectively controlled by the SNP in a bid to get around spending limits it would potentially be a breach of electoral commission rules."

The complaint centres around leaked emails in which it emerged that Mr Murrell had told BfS, which made a pro-enterprise case for independence, that he believed Ms Thomson and chief executive Gordon MacIntyre-Kemp had similar roles and that he "does not think that we need both of you". Ms Thomson later saw her consultancy payments stopped, although she was allowed to keep her title.

After details of the email emerged last week, sources at Electoral Commission said they did not believe the revelations warranted an investigation. However, it confirmed that it would now examine a complaint from Kevin Hague, the economics blogger and businessman who has previously claimed that BfS is a 'front' for the SNP.

A spokeswoman for the Electoral Commission said: "We have received a complaint and will be looking into it in line with our usual procedures."

While campaign groups are allowed to co-operate, joint working must be declared and spending would count against caps for both organisations. The rules are intended to prevent campaigners getting around spending caps by running multiple organisations.

BfS insisted that there was "absolutely no working together" with the SNP during the referendum campaign, saying it decided on its own spending priorities and tactics.

A spokeswoman added: "As the largest spender and most active campaigner of all the registered groups, BfS was probably subject to more scrutiny by the Electoral Commission than any other group. We reached out to and met with officials on many occasions. We had very productive and completely open and honest conversations. They took the view that BfS was a highly professional organisation and they gave our campaign a clean bill of health, in stark contrast to the No campaign’s business group who even tried not to register with the Electoral Commission.

"The accusations of working together are based on a total misunderstanding or deliberate distortion of the Electoral Commission's rules and its performance during the referendum. This is a panicked, cynical and groundless attempt to damage the Yes movement as support for independence increases both overall and amongst the business community, and as BfS goes from strength to strength."

Meanwhile, the First Minister pledged that she would not "jump to conclusions" over the property dealings of Ms Thomson which are the subject of a police investigation.

A solicitor, Christopher Hales, has been struck off for his part in 13 transactions that involved Ms Thomson, who denies any wrongdoing. A tribunal ruling stated that deals, in 2010 and 2011, potentially involved mortgage fraud.

Questions have also been raised over the morality of Ms Thomson's business model, which saw her purchase homes from people in financial distress and on occasion sell them on at a substantial profit within hours. Following May's election, she was appointed the party's spokeswoman on business, innovation and skills at Westminster.

Ms Sturgeon said: "I'm simply not prepared to jump to conclusions about an investigation that is currently under way. Even MPs are entitled to the presumption of innocence."

On questions over vetting of candidates, she said: "As a party we've quadrupled in size over the past year so that makes it all the more important that we make sure systems like vetting processes are robust and fit for purpose. We will learn any lessons that require to be learned."