The chief executive of the Police Ombudsman for NI has resigned from his £90,000 a year job.
Sam Pollock claims the office's independence has been undermined by meddling from senior civil servants at the Department of Justice.
In a statement, the Department of Justice said it had always respected the office's independence.
The ombudsman also strongly rejected claims the office's independence had been undermined.
Al Hutchinson said the independence of the ombudsman was "guaranteed by law" and he could confirm that "independence is both real and practical, as demonstrated by our reports".
"If it were otherwise, I would say so," he added.
The Department of Justice said that proper arrangements were in place to meet the accountability arrangements for public money.
It said if there was evidence to suggest any official had behaved improperly that would be looked into fully, but no such evidence had been presented.
Mr Pollock alleges he was subjected to malicious personal attacks after raising his concerns.
He was at Mr Hutchinson's side in February, when the ombudsman published his second, revised report into the murders of 15 people in McGurk's bar in 1971.
However, he wrote to the ombudsman just over three weeks ago announcing that he had decided to resign - and making it very clear that he is unhappy with the way the office is being run.
It is understood that his letter contains strong criticism of the relationship between the ombudsman's office and the police and senior civil servants, since Mr Hutchinson took over the job almost three-and-a half years ago.
It suggests the independence of the office has been compromised.
Mr Pollock has been chief executive since the office opened ten-and-a-half years ago.
He is leaving the post at the end of August.
His resignation is a major embarrassment for Mr Hutchinson.
Mr Pollock has a long and distinquished career within the criminal justice system, stretching back more than 40 years. That service was rewarded with an OBE in 2005.
Questioning the independence of the office and suggesting that senior civil servants influence the way business is done, are extremely serious allegations.
The independence of the ombudsman is viewed as a crucial factor in improving nationalist confidence in the police.
In a statement, Al Hutchinson paid tribute to Mr Pollock, saying his dedication, commitment and leadership had contributed to a reputation for the office as a world-class oversight agency.