The company's Free Basics service lets people in some countries access Facebook and some other websites without charge.
But critics of the service say it undermines the principle of net neutrality - the idea that all internet traffic should be treated equally.
Facebook told the Associated Press it was working to resolve the situation.
Egyptian mobile network Etisalat began offering the Free Basics service to mobile customers two months ago.
It allowed people to access Facebook and other participating websites without paying for mobile data, which can be expensive in Egypt.
Facebook said three million Egyptians had used the service, with a million of those going online for the first time.
But critics say internet providers and mobile networks should not be offering cheaper or faster access to selected services.
In December, the telecoms regulator in India asked mobile networks to suspend the scheme in the country while it considered granting it specific approval.
Facebook chief Mark Zuckerberg responded to critics in an editorial he wrote for the Times of India.
"Instead of welcoming Free Basics as an open platform that will partner with any telco, and allows any developer to offer services to people for free, they claim - falsely - that this will give people less choice," he said.
"This isn't about Facebook's commercial interests - there aren't even any ads in the version of Facebook in Free Basics."
By: BBC.