THE head of the UK civil service has denied Sir Peter Housden, Permanent Secretary to the SNP Government, was being frozen out of high level Whitehall talks about Scottish independence.

Last October, Sir Peter was accused of abandoning the traditional role of civil service impartiality and of "going native" by backing the Scottish Government's policy for independence.

The row erupted in the House of Lords with at least one peer calling for Sir Peter to resign. All three opposition party leaders at Holyrood wrote to Sir Gus O'Donnell, the then head of the civil service, expressing concern about what they saw as its politicisation in Scotland.

Sir Gus duly examined the matter and backed his colleague, but last month the issue flared up again as it was suggested Sir Peter had told officials he expected First Minister Alex Salmond to win the 2014 independence referendum.

Once again, opposition politicians aired concerns about the lack of civil service impartiality, which were met by denials from the Scottish Government.

It insisted Sir Peter had been "simply stating that if there is a positive result in a referendum, negotiations and legislation will follow".

The latest claim is that Holyrood's Permanent Secretary has been left out of Whitehall discussions on Scottish independence because his fellow mandarins feel they can no longer have "free and frank discussions" on Scotland while he is in the room.

One UK Government source described such a position as "entirely logical" given the policies of the administrations in London and Edinburgh were at opposite ends of the spectrum on Scottish independence.

Another source admitted that, as the referendum neared, it would be harder to exchange ideas.

Sir Bob Kerslake, head of the civil service, and Sir Jeremy Heywood, the Cabinet Secretary, issued a joint statement, insisting claims Sir Peter had been frozen out of Whitehall talks were "wide of the mark".

They said: "Far from being shut out, Sir Peter is a very experienced and valued member of the top team, who regularly attends the Wednesday morning meeting of Whitehall permanent secretaries."

They add: "The debate on independence will no doubt be a lively one but we are a single civil service and we will continue to support our respective administrations through this period according to our core values of honesty, impartiality, integrity and objectivity."

They point out Sir Peter had recently been asked to sit on the new Civil Service Board, which will provide strategic leadership for civil servants, give collective advice to ministers and, where appropriate, take decisions on behalf of the service.

Last Thursday, Sir Bob and Sir Jeremy were in Edinburgh to meet staff. Their visit included a meeting with Mr Salmond.

A Scottish Government spokesman told The Herald that the suggestions Sir Peter should not attend meetings of senior civil servants because of concerns about his impartiality were not discussed at the meeting, which was "part of a routine visit".