Dr Paul Molloy spoke out as the NI Department of Health, the Medicines and Healthcare products Regulatory Agency (MHRA) and the World Health Organisation (WHO) said evidence “does not suggest” the jab causes clots.
Irish officials said the move was precautionary following reports from Denmark and Norway about blood clots in some people who had been vaccinated.
Manufacturer AstraZeneca has said there is no evidence of a link between the two.
As of March 10, there were just 30 reports of clots among almost five million people given the vaccine across Europe.
The development coincided with the announcement that people aged 50 or over in Northern Ireland can now book their Covid-19 vaccine appointment.
Booking slots are available at regional vaccination centres across NI and they will primarily be using the AstraZeneca vaccine for first doses, to maximise available vaccine supplies. Anyone who received the Pfizer vaccine as a first dose will still receive the Pfizer vaccine for their second dose.
Dr Molloy says people should still go and get their Covid-19 vaccine when asked to do so.
He told the ‘Journal’: “If I had a decision to make as to whether I’d get the vaccine, I’d be 100% happy to do so... If you get the Covid virus and are laid up in bed for a few weeks, your chances of getting a clot are many, many times higher than your risk with any vaccine.”