Garda chief Martin Callinan has warned there could be mass assassinations if the force's watchdog was given unfettered access to classified records.
The country's top police officer said he had "no crib" with the Garda ombudsman carrying out its role generally.
But the commissioner said he had legitimate concerns about how very sensitive details were handled.
In the latest twist in continuing tensions between the force and its official oversight body, Mr Callinan said the crux of the disharmony was down to how top-level intelligence was handled.
The police chief said he needed reassurance on certain disclosures to the ombudsman relating to informants.
"Otherwise we will have bodies lying all over the country," he said.
Mr Callinan was hauled before TDs and senators to answer charges that his rank and file were not co-operating with the official State investigators.
The commissioner warned it was the "nature of the game" that there would always be tensions between his force and its official watchdog.
This was because of the type of allegations being levelled against his officers and investigated by the ombudsman.
"Will there be tensions? Will there be issues? Of course there will," he told an Oireachtas committee.
But he added that he was more comfortable that both sides could move on in a spirit of co-operation after recent negotiations led to new protocols on the handing over of information.
Mr Callinan said one officer has been arrested by the ombudsman, while two Garda stations were searched - in Cork and Limerick - under powers handed over to the watchdog.
The Garda chief also denied any Garda informants are being run "off the books".
"If I find out about it I will deal with it and will deal with it in the most serious way," he said of any rogue officers.
There are very strict policies in relation to registering informants in the force's Covert Human Intelligence Source (Chis), Mr Callinan told the joint committee on public service, oversight and petitions.
But he refused to disclose how many people are currently on the system or how many Garda officers are running informants.