The US Secretary of State, speaking at the new £90 million Titanic centre which was built as a beacon of hope in Belfast's docklands, said the peace process was being challenged.
Her visit coincides with a period of high tension, as violence continued last night in Belfast after a decision to remove the Union flag from permanent display at the City Hall.
Mrs Clinton said: "What we have to do is get out of the ballrooms, out of Stormont and into the communities where people live, where they do not have that lasting hope of optimism."
The US politician, who was instrumental in Northern Ireland's peace process, said she wanted to continue to work with political leaders to help progress the peace after she stands down from politics next year.
She said: "I want to remain involved as a friend, advocate and cheerleader for what we already achieved. Let us reach out to those who do not yet feel in their heart what has been achieved."
Offices of the cross-community Alliance Party have been attacked in recent days over the flag dispute, with two bombs found yesterday in Londonderry and County Down.
Mrs Clinton met Alliance Party MP Naomi Long, who had a death threat from loyalists over her party's stance on the city hall flag.
Earlier, Mrs Clinton, on her seventh visit to Northern Ireland, said peace required sacrifices, compromise and vigilance and the events of the past week showed the work was not complete.
She said: "There will always be disagreement in democratic societies, but violence is never an acceptable response to those disagreements. All parties need to confront the remaining challenge of sectarian divisions peacefully together."
Yesterday afternoon Mrs Clinton addressed 500 guests at a Worldwide Ireland Funds lunch.
Among the guests were former first minister Ian Paisley, 1972 Olympic gold medallist Dame Mary Peters and Nobel Peace Prize winners John Hume and David Trimble.
Sinn Fein president Gerry Adams, PSNI Chief Constable Matt Baggott, Northern Ireland Secretary of State Theresa Villiers and North Antrim MP Ian Paisley Jnr were also there.
Security was tight, with armoured police Land Rovers parked outside the Titanic centre, close to where rioting erupted on Monday night.
Mrs Clinton said she was impressed by the steady, common-sense leadership provided by Northern Ireland's First and Deputy First Ministers in the mandatory coalition government at Stormont.
She was presented with a Worldwide Ireland Funds lifetime achievement award in recognition of her commitment to peace and reconciliation.
A bomb similar to those used against security forces in Iraq and Afghanistan was discovered in Londonderry, hours before Mrs Clinton arrived in Belfast.
Chief Superintendent Stephen Martin said the bomb could have ripped through an armoured patrol vehicle and killed police officers.
He said: "This is a weapon primarily designed to kill. These devices are used in places like Afghanistan and Iraq with deadly consequences."
The bomb was found after police stopped a black Renault Megane car in the Westway area of the Creggan estate about 8.40pm on Thursday.
Eyewitnesses said officers rammed the car, with three men in it arrested and a fourth held a short distance away.
Security chiefs believe dissident republicans opposed to the peace process were planning an attack in the centre of the city, next year's UK City of Culture.
Mr Martin said: "We believe it was likely intended to be used against police officers in this city."
Earlier this year, a similar projectile explosive device was discovered in the Ardoyne area of Belfast.