Peter Robinson and Martin McGuinness were in Brussels on Thursday to speak about how money from the EU PEACE Programme has helped the peace process.
Almost €2bn has been provided between 1995 and 2013, they said.
The conference looked at how the example of NI and the Border Region of Ireland could be adapted to other parts of the EU where bridging differences is a challenge.
However, in light of the violence that has erupted on the streets following the removal of the Union flag at Belfast City Hall, the leaders stressed that progress has not been damaged by the events of recent weeks.
DUP leader Mr Robinson said: "Recent events have shown that reconciliation and peace are very much still work in progress.
"But the lesson today is the same as it has always been - violence obtains nothing except harm to the perpetrators and the communities they claim to represent.
The difficulties of recent weeks must not be allowed to take the shine from the success of the tens of thousands of projects which have brought communities together in Northern Ireland in a spirit of reconciliation, hope and confidence in our future.
"Active politics and rational dialogue offer the only way forward. This is the view shared by all of the political parties in the Northern Ireland Assembly. It is only through dialogue in the absence of violence that situations can be worked out."
Since its launch in 1995, the funding has been used to promote reconciliation by boosting numerous community groups, as well as projects such as the Peace Bridge in Londonderry.
Sinn Féin's Martin McGuinness said PEACE has played a significant role on the road to reconciliation in the north.
"Recent events at home signal there is still work to be done," he said.
"We have come too far to lose momentum and the progress that we have made. We are committed to the rule of law and the primacy of the political process. We deplore violence on our streets and are determined that communication and reconciliation are central to our shared future."
The ministers spoke to an audience which included delegates from other divided regions looking for solutions - including the Balkans, Libya, the Basque region and Cyprus.
They highlighted that the PEACE programme has made a "tangible" contribution.
EU Regional Development Commissioner Johannes Hahn, who was in Derry in June 2011 for the opening of the Peace Bridge, told delegates he was "overwhelmed" by his trip.
He said he wanted those at conference to benefit from the achievements of Northern Ireland.
"I was overwhelmed by the people I met on that trip, people from both communities who bear the physical scars of the troubles," said Mr Hahn.
"People who a few years back wished each other only harm are now working hand in hand to build a new shared future. Their passionate commitment and sheer determination are truly laudable. This is why I wanted to bring their experience to Brussels.
"I want the widest possible audience for their achievements because I believe other parts of the world may be able to learn from their work".