After an attack on the US consulate in Benghazi killed the US ambassador to Libya and three other Americans, Libyan officials, including the interim president, rapidly and unequivocally condemned the attack, calling it “cowardly” and apologizing to the US. And after the US embassy in Yemen was attacked today, the Yemeni president promptly apologized.

But in Egypt, where an angry crowd breached the US embassy walls the same night and brought down the American flag, tearing it up and replacing it with an Islamist banner, the silence from Egyptian officials was deafening in comparison.

And when President Mohamed Morsi finally spoke out against the attack, it may have been too little, too late.

The embassy breach was an opportunity for Mr. Morsi, who still faces much skepticism abroad as Egypt’s first Islamist president, to reassure the US that he values America's friendship. His delayed, ambivalent response will likely rattle US officials and businessmen looking for signs of stability and undermine whatever trust he's managed to establish with them.

“I think it’s shocking,” says Michael Wahid Hanna, a fellow at the New York-based Century Foundation, of Morsi’s lack of response to the embassy breach. “I don't think they quite understand the damage they are doing at the moment.”

Morsi's first response didn't come until yesterday afternoon. Even then, in statements read by his spokesman and released on his official Facebook page, he did not condemn the breach of the embassy. Instead, he denounced the obscure anti-Islam film, produced by Coptic and evangelical Christians, that sparked the protests when it was publicized by Egyptian media, called for the filmmakers to be prosecuted, and said Egypt supports peaceful protests. He directed the Egyptian embassy in Washington to take “all possible legal action” against those who produced the film.

Morsi finally responded in person to the attacks today, in a recorded statement broadcast on state television in which he said he said Egyptians are free to protest, but not to assault embassies. At a press conference on a trip to Brussels this morning, he pledged to protect embassies in Egypt and promised not to permit such an attack to take place again, while again condemning the film.

Squandering US goodwill?

Just how much damage was done may have become clearer last night, when President Obama said in an interview with Telemundo that Egypt, with which the US has had a strong partnership for three decades, was not a US ally. “I don't think that we would consider them an ally. But we don't consider them an enemy,” said Obama. “…I think that we are going to have to see how they respond to this incident.”

The cool tone from the US could also be seen in President Obama's call to Morsi yesterday. Compared to his seemingly warm chat with the Libyan leader the same day, his call to Morsi, described in a White House release, appeared curt.

Obama “underscored the importance of Egypt following through on its commitment to cooperate with the United States in securing U.S. diplomatic facilities and personnel,” the release read. According to the White House, Morsi expressed his condolences about the deaths of four Americans in Libya, and promised to ensure the safety of the American embassy in Cairo, but did not apologize for allowing it to be breached.

The overrunning of the US embassy came at a particularly awkward time for Morsi – at the tail end of a trip to Egypt by a large delegation of American businessmen. The government hoped to portray Egypt as stable enough for desperately-needed investment.

After positive meetings with the American businessmen, “all of that goodwill and confidence in their ability to be good stewards of the Egyptian state is going to be squandered,” says Hanna. “And I think it reflects a real ineptitude and a lack of fundamental understanding of being national leaders on the international stage.”

To be sure, the Cairo embassy protest, which was nonviolent, was vastly different than the deadly attack on the consulate in Libya. Yet the sight of protesters raising a flag that has been used by Al Qaeda in the embassy compound, and of “Bin Laden” spray-painted on the embassy gate – after Egyptian police failed to keep protesters from overrunning the compound – is sure to stoke American anger.

Balancing interests

Like Morsi's statements, the responses by the Muslim Brotherhood and its political arm, the Freedom and Justice Party, appeared aimed at a domestic audience rather than an international one. The FJP, which Morsi led until he ran for president and is the most powerful party in Egypt, released a statement yesterday that said the film crossed the bounds of free speech, and called for the prosecution of those who insult “heavenly religions.” The Muslim Brotherhood itself called for peaceful protests against the film tomorrow.

Morsi’s silence is an indication of the public anger that this issue incites, as well as the pressure he faces from more conservative Islamists. Many Muslims consider any portrayal of the prophet Muhammad to be forbidden, so a film that mocks him and portrays him as an immoral buffoon is doubly offensive. Many in the region, where the freedom to insult religious symbols is not often recognized as a part of free expression, question why the US would allow such a film to be made and do not understand that such a movie could be made without the endorsement, or at least tacit approval, of the government.

At the same time, Morsi is facing competition from ultraconservative Islamists who have become influential in the post-revolution political world, and have challenged the Brotherhood’s claim to be the representative of political Islam. The protest at the embassy was called by called by members of the salafi sect, who practice a Saudi Arabian version of their faith. They were joined by non-Islamists, including some Christians and a group of hard-core soccer fans, who claimed responsibility for bringing down the American flag.

Morsi also faces pressure to break from the mold of the past, when former President Hosni Mubarak was seen as a puppet of the US. The new president has gone to great lengths to at least appear to chart a more independent course.

“Egypt is no longer a politically oppressed country, it's a politically free country. In a democracy, the will of the people has to be translated into political actions. This may help us understand some of what has happened here, and perhaps the delay of some of these statements,” says Gehad el Haddad, an advisor to the Freedom and Justice Party.

Morsi’s statement, says Mr. Haddad, shows that his first concern is his people, rather than the US. But he acknowledged that Morsi's reaction likely damaged relations with the US.

“In a standard situation when there's enough trust established between two nations, such incidents can be quickly resolved. But because of the volatility of the situation in Egypt, and the fact that we've been working on rebuilding the relationship with the US for the past two years on a basis of trust, it certainly is damaging to the US-Egypt relationship.”

He adds, "We find the violent protest to be wrong, and Friday's demonstrations should show Egyptian youth the right way to peacefully voice their anger."

Omar Ashour, an expert on Islamist groups at the University of Exeter, says the protest put Morsi in a difficult spot with his more conservative supporters, but he could condemn the embassy breach without appearing to brush aside concern about the film by admonishing protesters for holding the US government accountable for a film it did not produce.

In fact, that was the tack taken by Morsi’s prime minister, Hisham Kandil, who made the strongest statement here against the embassy breach yesterday. He said the incident was “regrettable” and “rejected by all Egyptians and cannot be justified, especially if we consider that the people who produced this low film have no relation to the government.”

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He also called on the US to take action against the filmmakers, “within the framework of international charters that criminalize acts that stir strife on the basis of race, color or religion."

But such statements, says Hanna, are too little, too late. “I think there's going to be a lot of damage, a lot of skepticism,” he said. “If you're an international business executive, what if that's your factory or plant under attack? You can be sure probably that no one's going to come up to bat for you if there's some sort of challenge to Morsi from the right. Populist Islamist sentiment is something he will never take on.”