John Boothman, the head of news, has come under fire from retired broadcaster Derek Bateman who said in his blog that his strong past links to the pro-United Kingdom party are a liability in today's Scotland.
Mr Bateman wrote of Mr Boothman, whose partner is the former Labour health minister Susan Deacon: "John Boothman was a clear asset to the BBC at that time because of his Labour connections. They were key to his career and were valued by all. He had the respect of all sides throughout his career as a producer.
"But I felt from the outset that in the febrile air of today's Scotland with so many political knives being sharpened, it was a risk to appoint as head of news someone around whom the perception of affiliation hung."
Mr Bateman is also critical of Mr Boothman's management role.
He added that he was determined to speak up about Mr Boothman, but as a former colleague "it still stings me personally to expose him".
He added: "I do so because complaining internally is proven to be useless and because when you reach executive level certain protocols are required, certain behaviour is expected.
"He has executive authority to affect the lives of staff and when that is used as ruthlessly as he has in ending the careers of friends and colleagues, he loses the right to loyalty."
Mr Bateman, a former Herald journalist, presented the BBC's Good Morning Scotland programme for 10 years and the Saturday current affairs review Newsweek Scotland. He reported from Brussels and Strasbourg for the BBC, and on the Troubles and worked around the world, covering two US presidential elections.
Mr Bateman's blogs have recently made headlines,with some of his observations making uncomfortable reading for senior figures at BBC Scotland.
A BBC source indicated last night: "Social media allows people to express a wide range of personal views on organisations, including the BBC, but we don't provide a running commentary every time that happens."