Education Minister Jan O’Sullivan and Equality Minister Aodhán Ó Ríordáin were unable to exit the premises for about 40 minutes as a small number of demonstrators blocked the way out of the school in North Dublin.
The ministers left their car to wait out the protest back inside Gaelcoláiste Reachrann in Donaghamede.
The demonstration is the latest in a wave of such protests which saw a meeting of Cork City Council suspended earlier this week after protesters entered the chamber.
Demonstrators also gathered outside the home of Fine Gael TD Ray Butler in Co Meath.
Taoiseach Enda Kenny condemned the action, saying it had terrified young children.
President Michael D Higgins was subjected to verbal abuse when he left a school in Dublin last month as demonstrators branded him a “midget” and a “parasite”.
A number of arrests have been made in connection with the most high-profile such protest which took place in November in South West Dublin when Tánaiste Joan Burton and a female assistant were trapped in a car for more than an hour.
Ms Burton said she had no problem with anti-water charge protesters demonstrating at this weekend’s Labour Party conference in Killarney, as long as they did so peacefully.
“Protest in Ireland is a cornerstone of our democracy and if they wish to come to Killarney I’m sure the hotel people and the hospitality people will welcome them,” she said.
“But we’re a democratic party and the essence of democratic politics is that people should respect that everybody who is involved in politics has the right to conduct their politics and to hold their party conferences.
“But of course people who want to protest, they’re free to protest wherever provided it’s done within our laws.”
Socialist TD Ruth Coppinger has accused the Government of trying to discredit anti-water protesters