Archbishop Pierbattista Pizzaballa, apostolic administrator of the Latin Patriarch of Jerusalem, said "dozens" of groups had pulled out of planned visits after being scared off by the announcement and subsequent clashes.
He added that the heads of the Christian churches in Jerusalem would find it difficult to accept an official request by US Vice President Mike Pence to visit the city's holy Christian sites in January, calling for him to "listen more" to other Christians.
"After this there are some tensions in Jerusalem, Bethlehem also. This scared many people, so we've had less people than expected."
He stressed, though, that they would continue with planned Christmas celebrations.
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Trump's recognition of Jerusalem, breaking with decades of US policy on one of the most complicated issues in the Israeli-Palestinian conflict, has been met with near-daily protests across the Palestinian territories.
Pizzaballa, the most senior Roman Catholic official in the Middle East, stressed the church was opposed to "unilateral" decisions on the future of Jerusalem.
Pence's team cited key votes on US tax reform as the cause of the delay.
Christian leaders across the Middle East had said they were no longer willing to meet with Pence, an evangelical Christian, following Trump's decision.
Asked whether Pence could visit the Holy Sepulchre, believed to be the site of Jesus's crucifixion, and other Christian holy sites in Jerusalem, Pizzaballa said it would be a "problem" if he wanted to come on an official visit.
"We cannot say no to pilgrims, we are religious, we cannot say no to someone, even if he is the bigger sinner in the world," he said.
He said Pence should "listen more. No one has a monopoly on Jesus, not even the Evangelicals.
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