John Robertson, a researcher at the University of the West of Scotland, claimed the BBC had threatened him following the publication of his study which concluded that there had been a three to two imbalance towards anti-independence statements in BBC coverage.
The Yes campaign was heavily personalised around Alex Salmond and anchors concluded with anti-independence statements that went unchallenged, Dr Robertson told Holyrood's Education and Culture Committee.
However, BBC bosses completely rejected the allegations, insisting the report contained factual inaccuracies with quotes from people who did not feature in its reports and lines that its journalists did not say.
BBC Scotland director Ken MacQuarrie said Mr Robertson refused the BBC's requests for his raw data.
Head of news and current affairs John Boothman denied that the study had been suppressed, pointing out that Dr Robertson had discussed it on BBC Scotland's flagship morning news show and that it was debated in phone-ins.
He acknowledged that complaints about BBC coverage had increased since the start of the referendum campaign but bosses were unable to provide MSPs with a breakdown of how many were referendum-related.
Dr Robertson said: "I would like to condemn the behaviour of BBC Scotland's department of policy and corporate affairs in suppressing the dissemination of my research, and in circulating an insulting and ill-informed critique of my research directly to my principal.
"I've been personally hurt by the combination of threat from a powerful institution, although there has been no horse's head in my bed yet, abandonment by the mainstream media and by academia other than my own immediate colleagues.
"I interpret the above as an attempt at thought-control."
Dr Robertson is a media researcher of 30 years' academic experience who describes himself as a socialist, pacifist, feminist, anti-imperialist Scottish independence supporter, who rejects the SNP for its pro-Nato stance and Labour for being "fatally corrupt".
Mr Boothman said the study contained "quite glaring" errors which had since been corrected in subsequent versions.
"There were either factual errors about the date, people named as taking part in the report didn't take part, the end summary, what we call the pay-off, of the report were not the pay-offs that were either said by the reporters or included in the reports," he said.
Mr MacQuarrie said: "We completely reject the allegations about our news coverage, as we do the questioning of our journalists' professionalism and what they have brought to air.
"The evidence it presents does not support the contentions that it makes and the conclusions are based largely on flawed analysis and occasionally intuitive guesswork."
He added: "We asked if we might see the raw data as we did not recognise the evidence presented as an accurate reflection of our broadcast output and the request was rejected by the report's author."
Mr Boothman said: "In the past couple of years with the onset of the referendum and in relation to some stories we have done on Scottish football, there has been a rise in the number of complaints that BBC Scotland has dealt with."
Committee convener Stewart Maxwell asked for a breakdown of complaints about referendum coverage.
Mr MacQuarrie said: "The BBC Trust regularly publish the data about the number of contacts on an annual basis. Specifically, we would not break down the complaints into subject by subject areas."