Rupert Murdoch's interest in winning independence for Scotland has ended. News International's top selling title in Scotland, The Scottish Sun – whose support is widely regarded as crucial to the "Yes" campaign in the run-in to the September 2014 referendum – will not be backing independence.

In a significant blow to Alex Salmond's attempt to close the gap on the current substantial pro-Union lead, senior management sources inside News International in both London and Glasgow told The Independent that The Scottish Sun, which backed Mr Salmond in his landslide victory at the 2011 Holyrood election, is not looking to back the SNP ahead of the 18 September vote next year.

The decision effectively draws a line under a four-year charm offensive by Mr Murdoch towards Scotland's First Minister and ends a friendly and unlikely alliance between the global media mogul and the pugnacious ringmaster of Scottish politics. The SNP's failure to continue being supported by the Sun, which sells around 300,000 copies north of the border, will force a rethink of the "Yes" campaign's strategy.

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The latest opinion poll puts support for independence at 36 per cent, support for Scotland to remain in the Union at 46 per cent, and those undecided at 18 per cent. With a shift away from any radical change widely expected to occur as the referendum gets closer, the "Yes" campaign technically needs to be close to 60 per cent within the next 12 months.

Mr Murdoch and News International formally maintain that the Sun's decision in 2014 will lie with the editor of the Scottish edition, Andy Harries. However Mr Salmond told the Leveson Inquiry last year that he knew London – in effect Mr Murdoch and his senior advisers – held a crucial veto on the issue.

A senior boardroom source at NI in London said "The Scottish Sun will not be backing the SNP on independence. We will have a neutral stance".

Mr Murdoch had tweeted last year "Alex Salmond clearly most brilliant politician in the UK," and met Mr Salmond at his official residence to discuss investing in Scotland. There have been five Murdoch-Salmond meetings in recent years, along with exchanged personal calls and letters, but there has been an effective silence between the two over the last 12 months.

The withdrawal of support for independence by Mr Murdoch also suggests he has rethought earlier calculations that Mr Salmond is a winner – routinely a pre-requisite for support by NI – and that any commercial advantages for News Corp businesses in backing the SNP can no longer be guaranteed.

The apparently close relationship between the First Minister and the News Corp boss was criticised in the Leveson Report. Lord Justice Leveson's examination of press conduct said that Mr Salmond displayed a "striking" willingness to lobby the UK government on behalf of the Murdoch empire and that during the attempted 2011 BSkyB take-over, Mr Salmond "stood ready" to contact ministers and to persuade them to support News Corp's takeover.

The Independent made efforts to contact Andy Harries, editor of The Scottish Sun, in Glasgow, however he was not available to comment.