The Innocence of Muslims film has sparked violent protests across the region, killing the US Ambassador to Libya.
Open Doors USA fears that already marginalised Christians could experience "severe consequences" as a result of the film.
"It illustrates how hot the fuel is that one spark ignites it so suddenly," says Open Doors spokesman Michael Wood.
"At some point we heard that people were protesting because of a film not even knowing what movie this was all about.
"And as was the case with the publishing of the Danish cartoon several years ago, the movie has been on the Internet several months.
"But it is the unpredictable momentum that suddenly creates a wave of protests and anger. Many of the Muslim fanatics link the US with Christianity. So that puts believers in these hot spots such as Libya and Egypt directly in the line of fire."
The Muslim Brotherhood has called for peaceful protests on Friday outside the main mosques of all provinces in Egypt to "to denounce offences to religion and to the Prophet".
With more protests on the horizon, Wood said that Christians in Egypt and Libya need prayers now more than ever before.
"Pray that the violence over this film does not spread to other countries. That is the number one prayer request," he said.