Professor Luke O'Neill has said wearing masks should continue in appropriate settings even if the legal requirement is removed.
The Trinity College Immunology expert made the comments following a recommendation from NPHET that all remaining public health restrictions should be removed.
An official decision on whether or not the measures should be removed will be made by Cabinet next week and could see the requirement to wear masks in shops and on public transport abolished.
It is understood the HSE Covid testing regime will also be scrapped for people under 55 who are otherwise healthy and will be confined to selected groups, including the vulnerable.
NPHET has also recommended the removal of all Covid measures in schools and childcare settings, including physical distancing and pods.
However, Prof O'Neill has warned that the decision could cause great upset for those who are vulnerable.
Speaking on Newstalk's Anton Savage Show, he said: "It's still wintertime, and the virus is still there. We should still encourage people to wear masks in indoor settings… It's just it's not going to be illegal anymore not to wear them.
"The ones we worry about now are the immunocompromised people… they're very worried. Public transport is a big fearful place for them."
Although Prof O'Neill said, Ireland's successful vaccination programme has put the country in a "fantastic place" as vaccines have eased the pressure of the healthcare system.
He said a Covid booster vaccine programme similar to the flu jab will likely be rolled out next year and will focus on vulnerable groups and older people.
"Flu's the great parallel, really - vaccinate the vulnerable every winter.
"Next winter, we can anticipate another vaccination campaign - just like flu, it will be in the vaccine schedule for vulnerable and older people. That vaccine might be against Omicron or might be a pan-coronavirus vaccine by then that can handle any variant."
He added: "I can't emphasise enough that we have an antiviral [as well] - if you're in your 30s and you get infected, take an antiviral, and it will handle the virus quite well."
