The warning was sent out following reports that cases of anthrax have now spread from continental Europe to Scotland.
Ireland traditionally has a close connection with Scotland in terms of supplies of heroin.
In 2000, 17 heroin users in Glasgow and eight in Dublin died from the same batch of heroin, which had been contaminated with a bacteria called clostridium. Anthrax, an infection caused by a bacteria, can be potentially fatal if not caught early.
In a previous outbreak, 119 cases were recorded in Scotland between 2009 and 2010, resulting in 14 deaths.
The detection of anthrax in Lanarkshire in Scotland this week has left an injecting heroin user in a critical condition after receiving treatment in hospital.
Five other cases have been recorded in Europe since early June, including three in Germany and one each in Denmark and France. One German case and the case from Denmark have died.
A statement issued by Dr David Cromie, consultant in public health medicine at NHS Lanarkshire, said it was possible anthrax may be circulating elsewhere in Scotland.
“The advice to drug users is to avoid all heroin use, which we recognise may be very difficult for drug users to follow,” he said.
“Muscle-popping, skin-popping, and injecting when a vein has been missed are particularly dangerous. Smoking heroin carries much less risk than injecting it.
“If there is any pain or swelling around an injection site, drug users should seek urgent medical attention,” he said.
The alert issued by the HSE, which carries the advice issued by the NHS, has been sent out to GPs, departments of public health, emergency consultants, consultant microbiologists, consultants in infectious diseases and HSE drug services.
It states: “Given that there may be a potential link with the recent anthrax cases seen in intravenous drug users on the continent there is a possibility contaminated heroin may have found its way into Ireland.”
A HSE spokesperson told the Irish Examiner that there had been no reports to date here.
Tim Bingham of the Irish Needle Exchange Forum, an information and advocacy group, said: “Definitely there would be a concern it would come here, especially since it has been traced to Scotland. It’s already been in Germany, France and Denmark, so it seems to be spreading.”