After weeks of disruption amid Union flag protests, Ms Villiers said it was vitally important that people recognise the body as a law-enforcing authority and respect its decisions.
"They have a difficult job, their decisions are always going to be sensitive and it's impossible to please everyone," she said.
"Whatever people think of their decisions, it is absolutely essential that they are obeyed, because the consequences of what can follow if we disobey those decisions could be catastrophic for Northern Ireland and the perception of Northern Ireland around the world."
The Conservative MP, who is in Dublin for talks with Tanaiste Eamon Gilmore, said it was important that the British and Irish governments work to break the sectarian barriers that still exist in Northern Ireland.
Ms Villiers backed comments from the Tanaiste who insisted that both administrations should pledge full support to the Parades Commission - particularly in the run-up to the marching season.
Ms Villiers also briefed Mr Gilmore, the Minister for Foreign Affairs, on the latest Union flag protest developments.
Mr Gilmore said a distinction needs to be drawn between those who have caused trouble and those protesters who have demonstrated peacefully. "It's fair to say that the number that has been involved in street violence is small," he added.
The Parades Commission, which rules on contentious marches, has its busiest period approaching with the start of the loyalist marching season in April.
Ms Villiers said 2013 could still be a good year for Northern Ireland - with the Derry-Londonderry City of Culture and the G8 summit in June. She said it would be "deeply regrettable" if riots were to flare up in relation to flags.