The Director of the Medical Bureau of Road Safety said he became aware of a problem with the breathalysers in the summer of 2014 and something "was not adding up".
Last week it emerged that more than 14,500 people who were prosecuted for road traffic offences are to have their convictions quashed as a result of the controversy over fixed charge notices and the exaggeration of garda breathalyser test figures.
Speaking on RTÉ's Morning Ireland, Professor Denis Cusack said that for every breathalyser machine, there is a mouthpiece and a new mouthpiece must be used for each test.
However, it was noticed that a large number of mouthpieces remained in stock, despite large numbers of breath tests recorded.
He said this was pointed out to gardaí in July 2014.
The Medical Bureau carried out a survey of 200 of the 1,200 breathalysers in August 2015 after discrepancies showing 400,000 tests were reported as being carried out, but just 200,000 mouthpieces were used.
He said gardaí were alerted in August/September 2015 and then carried out their own audit, which took some time.
Prof Cusack said the audit was a garda operational matter and the bureau does not get involved in garda matters.
After the gardaí had completed its audit, they asked for the bureau to share its database information about the devices, and their audit corresponded with the results of the Bureau's survey.
He said everyone is concerned and wants to put this right and a new generation of breathalysers will be used in future with added features.