THE Irish Government has reopened its Chancery to the Holy See as Minister Flanagan admits there are 'difficult conversations' to come between the states.
The Minister was speaking at the formal reopening in Rome on March 17.
The move follows the reopening of the the Embassy in the Vatican in 2014 as a smaller one-person embassy focused on international development.
Also in attendance at the reopening was Archbishop Paul Gallagher, the Holy See Secretary for Relations with States, and Irish Ambassador to the Holy See, Emma Madigan.
Speaking at the reopening, Minister Flanagan said Pope Francis was "unlike any other" and had used his voice "fearlessly."
"The Holy See stands at the centre of a global faith community of well over a billion people.
"Pope Francis is a voice unlike any other. He has used that voice fearlessly in challenging the world to vindicate human dignity and human rights, eradicate poverty and hunger, tackle climate change, end conflicts, support sustainable development and to stand up for the values we all hold."
However, the Minister also said Ireland and the Holy See had "different perspectives" and there will be "difficult conversations."
"Like all old friends, Ireland and the Holy See have some different perspectives. That is normal in a bilateral relationship.
"At times, we will have difficult conversations. But we will also have many fruitful conversations about our shared values.
"Fundamentally we each believe we have a responsibility to work towards a world that is just, fair, safe and sustainable.
"We share a belief in the importance of the multilateral system. We share a belief in a rules-based international order and the importance of dialogue and concerted action."
Minister Flanagan also welcomed Pope Francis' "landmark" Papal Visit to Ireland in 2018.
"I would like to take this opportunity also to reiterate our warm welcome for the intention of Pope Francis to visit Ireland next year for the World Meeting of Families.
"This will be another landmark moment and one that will be of huge importance to so many Irish people and I assured Archbishop Gallagher that we will support it however appropriate."
Taoiseach Enda Kenny confirmed the 2018 visit of Pope Francis to Ireland in November last year.
The Catholic World Meeting of Families — the world’s largest gathering of Catholic families — is staged every three years in a different location around the world.
The event, set up in 1994 by Pope John Paul II and attended by him, was also presided over by Pope Benedict XVI during his reign.
Pope Francis will continue the tradition of attending the gathering, which is likely to take place both in the RDS and Croke Park.
The Papal Visit will only be the second papal visit ever to Ireland. Pope John Paul II’s visit in 1979 was the first and only one to date.