The doctor, who worked as a locum in obstetrics and gynaecology in 10 hospitals across the country, later tested positive for the virus, which can be passed on through blood contact.
It can damage the liver and be potentially fatal if left untreated, but many people who are positive are unaware until internal damage is done.
The hospitals, which have not been named, have now been alerted by the HSE's head of health protection Dr Kevin Kelleher.
A spokesman for the HSE said patients would be notified and invited for a test if an expert group, which is examining the background to the case, deems they were at risk.
He said the "expert group is currently establishing the background to the case to identify what actions, if any, may need to be taken".
The investigation will aim to establish the degree of infectiousness, if any, of the doctor.
The doctor, who has been registered to work here since October 2008, was employed by an agency.
He worked in Galway University Hospital earlier this year, before the Savita Halappanavar tragedy.
The HSE played down the chances that a patient could have been infected.
It said a review of cases between 1997 and 2008 where doctors who treated patients turned out to have the virus showed all 2,000 who were called for testing were clear.
The risk of a patient getting the virus from a healthcare worker is between 0pc and 3.7pc.
The Hepatitis C scandal involving blood transfusion and blood products came to light in the early 1990s.
The blood product Anti-D, which was given to women to prevent them having blue babies, was contaminated with the virus.
Over 1,000 women were infected.
Since 2008 all new full-time staff employed by the HSE have to undergo testing for Hepatitis C, but this does not apply to agency doctors.