Last week, a judge ordered the government to block access to the video-sharing website for 30 days for its carrying of an anti-Islam video that set off deadly riots last year.
The ministry said this week it cannot block access to YouTube because of high technical costs, adding that it cannot legally monitor the content of social media websites.
The Association for Freedom of Thought and Expression in Egypt said Saturday that it too filed an appeal, calling the verdict "collective punishment."
YouTube has already blocked access to the film in Egypt because it broke local laws.
Past Egyptian verdicts banning websites deemed offensive were similarly not implemented.