The U.S. Embassy in Cairo got into a very public digital dispute Wednesday with the Egyptian government -- as well as State Department headquarters -- over a tweet that linked to a "Daily Show" video mocking Egyptian President Mohammed Morsi.

The segment was a monologue by Jon Stewart on the arrest of an Egyptian satirist. Even though the State Department has spoken out strongly on behalf of satirist Bassam Youssef -- making an argument roughly in line with what Stewart talked about -- the tweet sparked a diplomatic flare-up.

The U.S. Embassy temporarily shut down its Twitter feed over the incident. When the Twitter feed returned, the "Daily Show" tweet had been scrubbed from the site.

The incident was the latest to raise questions about the operation of the sometimes wayward U.S. Embassy Twitter account but also whether U.S. officials were unduly pressured by the Egyptian government.

Morsi's office and the political wing of the Muslim Brotherhood had publicly complained about the U.S. Embassy's comments. Morsi's office wrote on Twitter that "it's inappropriate for a diplomatic mission to engage in such negative political propaganda."

State Department spokeswoman Victoria Nuland, in Washington, was peppered with questions Wednesday afternoon about the incident. She explained that the embassy should not have taken down its Twitter account and was effectively told by headquarters to bring it back online.

"There was an instruction that taking down the Twitter feed altogether was not in line with department policy," she said.

At the same time, Nuland suggested that State Department headquarters and the leadership at the embassy in Cairo had concerns about the decision to tweet a link to Stewart's show in the first place.

"I think that they ... came to the conclusion that the decision to tweet it in the first place didn't accord with post management of the site," she said, adding: "As you know, the decisions about Twitter content are made out of post. I can't speak to the decision to retweet Jon Stewart to start with."

The incident put State Department headquarters in a tricky situation. Nuland on Monday had assailed the Egyptian government for the arrest of Youssef, raising concern that freedom of expression was being "stifled."

"This coupled with recent arrest warrants issued for other political activists is evidence of a disturbing trend of growing restrictions on the freedom of expression," she said Monday. She added: "There does not seem to be an evenhanded application of justice here."

This tracked with what Stewart said in the video temporarily linked on the embassy's Twitter account -- though Stewart used more charged language. In the segment, Stewart said Morsi "would not be in a position to repress" people like Youssef if it were not for people like him protesting against former leader Hosni Mubarak.

"When you are actually powerful, you don't have to be petty," Stewart said.

Nuland said Wednesday that the State Department stands by its own criticism of Morsi. Secretary of State John Kerry also said Tuesday that the U.S. has "real concerns" about recent events in Egypt.

As for this particular Twitter account, Nuland said the embassy is "reviewing its procedures."

The Cairo Twitter account previously came under criticism during the Sept. 11 protests against, and attacks on, U.S. embassies and consulates last year. The Cairo embassy at the time tweeted messages condemning an anti-Islam film that was believed to be the cause of the protest in Cairo, which some criticized as an apology.