In a statement to The Associated Press, Facebook said it hoped to "resolve this situation soon" so the program, which it had launched with Etisalat Egypt some two months ago, could be restored.
"We're disappointed that Free Basics will no longer be available in Egypt," it said. "More than 1 million people who were previously unconnected had been using the Internet because of these efforts."
The service, which is aimed at users in developing countries, connects a billion people worldwide, providing free health, education, and economic information.
It was not immediately clear why the program was halted. Neither Etisalat nor Egyptian officials could immediately be reached for comment. The program was recently highlighted at an entrepreneurship fair in Cairo.
Facebook and other social media sites are extremely popular in Egypt, and were used to organize protests during the 2011 uprising that toppled longtime autocrat Hosni Mubarak.