Garda Commissioner Martin Callinan has rejected a claim by the Garda Ombudsman that informant handling systems can be bypassed or ignored.
Mr Callinan said that he has instructed that all informants are handled through formal channels and must be referred to the CHIS system, which manages informants.
He also said it is garda policy that all informants are told they may not act as 'agent provocateurs' entrapping others, or commit crime.
The commissioner said there is a difference between registered informants and public-spirited citizens who give the gardaí information on a once-off basis.
He also told an Oireachtas committee gardaí have spent €1.3m this year on conducting investigations for the Garda Ombudsman, and over €9m since the ombudsman was established in 2007.
Fine Gael’s Charlie Flanagan asked about the relationship between An Garda Siochana and the Garda Siochana Ombudsman Commission.
He said he was shocked to see an editorial in a garda magazine saying that there is a complete lack of confidence in the GSOC.
Speaking about informants, Mr Flanagan asked if the practice of "running informants off the books" was still evident.
Mr Callinan said that he regarded the issue as so serious that he choose not to make public comment.
Speaking about the relationship with GSOC, Mr Callinan said that the fact that the gardai may not see eye-to-eye with the GSOC on certain sensitive matters was something that needed to be worked through.
He said that the need to disclose the identity of an informant is a very serious matter as he would be putting a life or lives at risk by disclosing the identity without knowing exactly what was going to happen to that information.
He said that he has to be sure that the information is handled in a particular way and not disclosed to a third party.
He said that is the reason why he has been looking for guarantees about the way that information has been handled.
The Commissioner said that has caused difficulty in relation to some delays in dealing with GSOC.
He said that the new Memorandum of Understanding between the two bodies means that he hopes that the two bodies can "move on in a spirit of co-operation".
He said there are meaningful discussions going on with the commission.
Meanwhile, Minister for Justice Alan Shatter has confirmed his department will need a supplementary budget of €32m.
He said that there is an additional €51m required for the garda vote and €5m for the Magdalene women but almost €24m of that has been offset by saving elsewhere in the department leaving a sum of €32m required from external funding.