The Conference of European Churches (CEC) and the Commission of Bishops' Conferences of the European Union (COMECE) also highlighted how local churches have been supporting arriving refugees and the importance of reuniting separated family members.
Their joint delegation met with the Maltese Prime Minister, Dr Joseph Muscat, as Malta begins its six month Presidency of the Council of the European Union.
Migration and refugees dominated the hour-long summit, with both Maltese government representatives and church leaders agreeing that discourse needed to be reframed, with opportunities to welcome refugees and the benefits of migration for European societies each being promoted.
After five years of civil war, more than 4.8 million Syrians are currently registered refugees, according to the United Nations High Commissioner for Refugees.
The CEC and COMECE also encouraged the Maltese government to consider the "root causes" of the displacement of people, including environmental factors.
The CEC-COMECE delegation encouraged Malta to take a "holistic, global approach" in pursuing its priorities during the president.
The Archbishop of Malta, Mgr Charles J Scicluna, said: "Malta's Presidency of the Council of the European Union offers our nation the opportunity to give a strong impetus to revitalizing faith in the European project."
Under Article 17 of the Treaty of the Functioning of the European Union, the EU is obliged to hold "open, transparent, and regular dialogue with churches and religious communities".