The Pope made his comment in an address to other Christian leaders in Australia, where he is presiding at the Roman Catholic Church's World Youth Day celebrations.
"I think you would agree that the ecumenical movement has reached a critical juncture," he told representatives of various Christian Churches in Australia, including Anglicans, Lutherans and Methodists.
While he did not elaborate on his comment, the Pope appeared to be referring to the crisis gripping the 77-million-member worldwide Anglican community, with which the Vatican is engaged in dialogue aimed at eventual Christian unity.
The Anglican communion is deeply divided over the issue of gay bishops and women bishops.
A quarter of the world's Anglican bishops have boycotted the Lambeth Conference, the once-a-decade gathering of Anglican leaders being staged in the English cathedral city of Canterbury, spiritual home of the Church.
Liberal and conservative clergy have been brought to the brink of schism over the ordination in 2003 of Gene Robinson in New Hampshire, the first openly gay bishop in the Church's 450-year history.
Conservative Anglican leaders staged their own conference in Jerusalem last month at which they pledged to form a council of bishops to provide an alternative to churches who they say are preaching a "false gospel" of sexual immorality.
The Global Anglican Future Conference (GAFCON) said member churches would continue sponsoring breakaway conservative parishes in the liberal Western member countries and called for a separate conservative province in North America.
Archbishop of Canterbury Dr Rowan Williams, the worldwide Anglican leader, also faces another battle in the Church of England, the Anglican mother church, over plans to ordain women bishops.
Those plans have sparked threats of a mass walkout by conservative clergy and some have expressed a desire to convert to Catholicism.
The Catholic Church does not allow women priests, saying that Christ willingly chose only men as his apostles.
The Pope has already publicly expressed his concern over the future of Anglican Church, telling reporters aboard his plane earlier this week that he hoped it could avoid a schism.
"My essential contribution can only be prayer," he said. "The desire is that schisms and new fractures can be avoided," he said, adding that Catholic Church would not "intervene immediately" in their decisions.
In his address on Friday, the Pope said "we must continually ask God to renew our minds" in the search for Christian unity.
