Dr Tony Holohan told the transport committee that as case numbers continue to decline, the risk of re-importing the virus will become more significant.
While Ireland is starting to regain control of the virus, the situation in other EU countries is worsening.
Final preparations are being made to roll out the EU traffic light system for air travel on Sunday.
Dr Holohan says he understands the impact the restrictions have on families and the aviation industry.
"We're simply trying to in as dispassionate and as evidence based a way as possible, simply advise on what we think the risks are and how best to ameliorate and address those risks," he said.
"So we can have the best assurance that in this country if we make the progress that we think we can make over the course of the coming weeks, that we don't put that at risk by arrangements that we put in place over the course of the month of December."
