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"The church’s conscience came a bit late," he said.
During the incident, they played 'Middle Eastern music' and uttered slurs against Muslims, according to the Chicago Tribune.
The Vatican adviser has come under attack from right-wing groups.
The call came after Trump doubled down on his remarks after Charlottesville.
The pastor resigned the day Trump made controversial comments about Charlottesville.
"God has endowed rulers full power to use whatever means necessary — including war — to stop evil,” pastor Robert Jeffress said.
Evangelical leaders usually use their voice on specific issues, not to praise specific administration officials.
The pope and the president have clashed in the past.
They also discussed health care, support for Israel and other issues.
Darwin Martinez Torres, 22, of Sterling is being held in the death of Nabra Hassanen.