Nuala O'Loan was embroiled in another battle last night after the Director of Public Prosecutions refused to prosecute two police officers for perjury.
Although a Police Ombudsman's spokesman last night refused to comment on the alleged rift it is understood that serious tensions exist between the DPP and the ombudsman's office.
The row comes after an Irish News story in March last year revealed that of the 6,000 complaints made against police officers from 1996 to 2002 just nine officers were successfully prosecuted by the DPP.
And it is understood the ombudsman's office is studying its remit to see if it can petition the secretary of state to force the DPP to proceed with the perjury charges against the two police officers, one of whom is retired and the other still serving.
The controversy centres on the case of John Boyle from the Markets area of Belfast who was jailed for 12 years for a gun attack on a police patrol in 1976.
Mr Boyle was alleged to have made a verbal admission, during police questioning, of his involvement in the attack. At his trial he denied making any admission of guilt but was found guilty solely on the alleged admission.
In 1999 Mr Boyle's conviction was investigated by the Criminal Cases Review Commission (CCRC) and forensic tests carried out on the policemen's notes found they had been altered.
When Mr Boyle's solicitors requested access to case papers they were told the documents had been destroyed.
But ombudsman investigators found the "destroyed" papers in Newry, Magherafelt, Belfast and Liverpool.
The ombudsman then recommended to the DPP that the two police officers alleged to have been involved in altering the interview notes stand trial for perjury.
But a spokesman for Mrs O'Loan's office last night confirmed that it had been officially informed by the DPP's office that no charges would be brought.
"It is up to the DPP to make a decision whether or not to prosecute," the spokesman said.
"We will now look at the file again to see if there are any misconduct issues which would have to be dealt with (against the serving officer)."
Mr Boyle said he was instructing his solicitors to seek a judicial review of the DPP's ruling and questioned the implications for the ombudsman's office.
"The DPP asked the ombudsman to investigate my case and they recommended perjury charges be brought against these two officers," he said.
"The ombudsman's office was supposed to be an independent body set up to investigate miscarriages of justice by the police.
"I was jailed for 12 years solely on interview notes which have been found to have been altered by the police.
"Where is the justice and what powers does the ombudsman's office really possess?"
A DPP spokesman said the case had been dropped as it was not felt that sufficient evidence existed to secure a prosecution.
