The mysterious bugging of the Garda Síochána Ombudsman Commission started off as a controversy that threatened the reputation of the Garda but last night it appears that it may have damaged the reputation of the commission itself.

The confirmation by commission chairman Simon O’Brien that it had discovered three threats to its security system at its Abbey Street headquarters in Dublin raised as many questions as it answered.

Mr O’Brien said the commission had found no evidence of Garda wrongdoing in regard to the security breaches – which begs the question as to why the Department of Justice was not kept informed of the investigation.

A statement from the commission said: “We took the difficult decision not to report this matter to other parties.

“We did not wish to point fingers unnecessarily and we did not believe that widespread reporting would be conducive to public confidence. We took the decision not to report in good faith.

“We regret that now and this was communicated to the Minister for Justice and Equality by Simon O’Brien, chairman of the commission,” the statement said.

It is probably fair to say that if the Department of Justice had been informed of the matter, the Garda would have found out almost immediately – but that points up a disquieting level of distrust between the commission on the one hand and the Garda authorities and the Department of Justice on the other.

The fact that the commission secretly brought in a British company, Verrimus, which uses retired British security personnel, to assess whether its security had been penetrated indicates just how deep the level of distrust has become.

It is probably no great surprise that the Garda and those charged with supervising its behaviour should be at odds, but the level of animosity appears to have got completely out of control.

It appears that when the commission was established in 2006, it was advised that, on the basis of international experience, it should expect to be placed under surveillance, whether in the form of double agents, phone-tapping or data- interception.

While this was regarded as a bit far-fetched at the time, precautions were taken by the commission and one floor of its headquarters on Abbey Street was designed with security in mind.

In its statement, the commission said it had conducted two security sweeps since then, the most recent one in September of last year.

While the Garda was not directly accused after the publication of the bugging story at the weekend, it was widely assumed in the commentary on the story that the force was the prime suspect in the case.

The reaction of Taoiseach Enda Kenny and Minister for Justice Alan Shatter was to circle the wagons and put the focus back on the commission to explain itself. Kenny said it was very important to get to the bottom of why suspicions were raised in the first instance and why the commission board had responded as it did.

He insisted that section 80, subsection 5, of the Garda Síochána Act required that the commission should report unusual matters or matters of exceptional importance to the Minister for Justice.

“That’s a fundamental issue that GSOC needs to explain to the Minister,” the Taoiseach added.

The Act is actually a bit ambiguous on the point.

It states that the commission “may make” any reports that it considers appropriate for drawing to the Minister’s attention “because of their gravity or other exceptional circumstances”.

The Act adds that as soon as practicable after receiving a report under this section, the Minister shall cause a copy of the report to be laid before each House of the Oireachtas.

The commission’s expression of regret last night at the decision not to inform the department of the matter appears to be an acceptance of the Taoiseach’s point that the issue should have been brought to the attention of the Minister.

On the political front, the reflex action of the Government to defend the Garda came as no surprise and neither did the automatic reflex of the Opposition to blame the Government for whatever had gone wrong.

By going out of his way yesterday to insist that the sophisticated equipment involved in the bugging could have been obtained by private individuals or organisations, the Taoiseach was clearly intent on stopping people from jumping to conclusions.

The statement from the commission last night reinforced the message.

The Cabinet will get a full report on the matter today from the Minister for Justice and questions will undoubtedly be raised in the Dáil.

There is probably more to come in this controversy.