Speaking in Brussels on Tuesday at a meeting with religious leaders of the Christian, Jewish and Islamic faiths, Merkel said she "would like to have such a reference in the treaty ... but there are not many chances left."
Merkel, the daughter of a Protestant pastor and the leader of Germany's strongly Catholic CDU party, has been pushing strongly for a reference to Christianity in the new charter.
However, any attempt to mention Christianity or God in the treaty has been strictly opposed by secular France, liberal countries such as Sweden and Denmark and by Britain.
During the 2004 negotiations on the bloc's original constitution, there were concerns that any religious reference could anger Europe's Muslims and Jews.
Merkel, who currently holds the six-month rotating EU presidency, wants member states to agree to a mandate for a new treaty at the next European summit in June. The original draft was ratified by 18 of the 27 EU member states, but was vetoed by French and Dutch voters in 2005.
Portugal behind Merkel
Foreign Minister Luis Amado of Portugal, which assumes the EU presidency in July, urged fellow member states on Tuesday to swiftly agree on a new treaty of sorely-needed reforms for the bloc.
Presenting the priorities for Portugal's six-month turn at the EU helm, Amado stressed that the 27 EU nations "need a new treaty and we need it fast".
He said he hoped that the current German EU presidency, which ends on June 30, "succeeds in working out a new agreement and a clear mandate".
If that is done then the Portuguese presidency will make it their priority to deliver a new constitution, he told reporters, stressing the original charter should form the basis of its successor.
"The basis for this treaty is not to be invented. We got a strong consensus on the constitutional treaty and that should be the basis of a new agreement," Amado said. Portugal itself never ratified the original constitution.