Stewart slammed Morsi on the "Daily Show" Monday for arresting Bassem Youssef, the man known as "Egypt's Jon Stewart," for insulting Morsi and Islam on a similarly-themed comedy show.
"Democracy isn't democracy if it only lasts up until someone makes fun of your hat," Stewart said.
The Muslim Brotherhood responded with a post saying its Freedom and Justice political party objected to the American embassy's post as "flagrant meddling in #Egypt' domestic affairs." In a separate post, the party wrote: "Another undiplomatic & unwise move by @USEmbassyCairo, taking sides in an ongoing investigation & disregarding Egyptian law & culture."
Morsi's office also denounced the U.S. Embassy for the "Daily Show" post. "It's inappropriate for a diplomatic mission to engage in such negative political propaganda," the president's office wrote.
That post appears to have been removed. U.S. Ambassador Anne Patterson had the original post taken down, too, Foreign Policy Magazine's Cable Blog reports. State Department officials want it restored, the blog says, to avoid any appearance that online pressure led to its removal.
Morsi's office issued a statement on its Facebook page Wednesday denying that he had anything to do with charges being brought against Youssef.
"The Presidency reiterates the importance of freedom of expression and fully respects press freedom. All citizens are free to express themselves without the restrictions that prevailed in the era of the previous regime," the statement said. "The first legislation passed under President Mohamed Morsy was concerned with the prevention of pre-trial detention of journalists. This demonstrates the determination of the President to encourage press and media to operate in a free environment.
"We urge citizens to exercise their legal right to freedom of speech while respecting the rule of law."
Closer to home Mohamed Elibiary, a member of President Obama's Homeland Security Advisory Council, took issue with media attention on Youssef's arrest.
"A lot of AstroTurf advocacy in media on this," Elibiary wrote on his Twitter feed Tuesday. In politics, "AstroTurf" is a cynical term describing well-funded campaigns deceptively designed to appear to be grass-roots driven.
Elibiary was accused by Egypt's El-Rose Youssef magazine in December of having ties to the Egyptian Muslim Brotherhood.