Plans to include such a reference in the original EU treaty, rejected by French and Dutch voters in 2005, were blocked by Jacques Chirac, the French president.
Merkel, as holder of the EU's rotating presidency, is now in the process of reviving the constitution.
Comments from Merkel, the daughter of a pastor, have encouraged religious leaders around Europe to redouble efforts to modify the constitution.
Romano Prodi, Italy's prime minister, also said he had pushed for inclusion of Catholic roots in the European Constitution, but that the main task ahead for Catholics was to carry on a dialogue with religions like Islam and Judaism.
Prodi on Saturday, said: "I fought silently and for long for the insertion of Christian roots in the European Constitution."
The signing on Sunday of the Berlin Declaration is to be livened up during the weekend with cultural events throughout the German capital.
Museums will open their doors to the public into the small hours on Sunday while the city's discotheques will fire up a European Club Night.
And a festival at the Brandenburg Gate, a symbol of European division, then unity after the Berlin Wall fell in 1989, will feature national delicacies from each of the member states and a rock concert.