Dr Ronan Glynn has said that he is 'concerned' about the potential of future protests after the violent scenes in Dublin at the weekend.
A staggering 24 people have been arrested after a large crowd gathered at Grafton Street in protest of current restrictions.
A number of gardaí were attacked as the incident turned violent, with one member of the crowd setting off a firework in the direction of an officer.
And the groups behind the protests have already indicated there will be similar events in Cork this weekend.
They are also planning another gathering in Dublin on St Patrick's Day.
But the Deputy Chief Medical Officer has warned them off doing so.
"Broadly, what happened shouldn't have happened and shouldn't happen again," he told reporters at a press briefing in Dublin.
"The key message from our perspective is: the silent majority in this country are fed up, annoyed and do not want the pandemic to go on for a day longer - but they are sticking with restrictions. They are doing it quietly in their communities.
"That's the message the majority need to remember when they see the actions of a small minority.
"I'd be concerned (about future incidents).
"There are people who were frustrated in there, but not all of their issues can be addressed."
Dr Glynn also spoke directly to anyone who attended the event at the weekend.
He added: "I'd ask them to reflect on what the population as a whole has done over the last year. Be proud of what the country has done, rather than focus on the negativity and the messaging of a minority."
Meanwhile, one further Covid-19 related death was confirmed by health officials on Monday evening.
Another 687 new cases of the deadly virus were also announced by the the National Public Health Emergency Team.
The news comes as the phased reopening of schools began from today.
Over 320,000 primary school and Leaving Cert students returned to classrooms as the government aims for a full return in the coming months.
Special schools also moved to full capacity today, having for the past two weeks welcomed just half of pupils on alternate days.
