The U.S. ambassador to Egypt has become a lightning rod for criticism among Egyptians who accuse her of embracing the deposed Muslim Brotherhood-led government, even as a popular uprising was building against it in the streets of Cairo.

At last week’s protests against Egypt’s first democratically elected president, Mohammed Morsi, some of the anger was directed against Ambassador Anne Patterson and President Obama. Among the millions of protesters who packed into Cairo’s Tahrir Square, some held images of Mrs. Patterson and Mr. Obama with crosses marked across their faces.

Their anger was fueled by a June 18 speech in which Mrs. Patterson welcomed the opportunity to “set the record straight” on the U.S. relationship with the Muslim Brotherhood and expressed skepticism over the virtues of protests, which were just beginning at the time.

“Some say that street action will produce better results than elections,” Mrs. Patterson said. “To be honest, my government and I are deeply skeptical.”

Less than three weeks later, the military toppled Mr. Morsi’s government after four days of massive protests.

“Ambassador Patterson came up with statements that seemed to be dismissive of the uprising,” said Bassem Sabry, an Egyptian political commentator. “She didn’t seem to know how to react to the situation and wasn’t pleasing anyone.”

“The U.S. administration has a very bad favorability in Egypt. Even Mr. Obama’s ratings have dipped to historic lows since his speech at Cairo University [in 2009], so dissatisfaction with Anne Patterson reflects dissatisfaction with the Obama administration,” Mr. Sabry added.

Many Egyptians thought the Obama administration was interested in supporting the Morsi government only to ensure protection for its interests in the region, such as Egyptian peace with Israel.

‘That’s part of her job’

Michele Dunne, director of the Atlantic Council’s Rafik Hariri Center for the Middle East, said that while criticism of the Obama administration’s Egypt policy is valid, Mrs. Patterson was doing what is expected of almost any ambassador: cultivating the best possible relationship with the host government.

“I have no indication that she was doing anything other than what the administration wanted her to do,” Ms. Dunne said.

She faulted the Obama administration for not doing enough to reach out to opposition and civil society groups.

“The opposition felt puzzled by how few contacts they got from the U.S. and how superficial these contacts were,” she said. “They often felt that American visitors — from the administration as well as Congress — were just checking the box by meeting a representative from the opposition and that there was no genuine interest in engaging them.”

On Wednesday, the leader of the ultraconservative Salafist Nour Party, Younis Makhioun, denied reports in the Egyptian media that he had struck a deal with Mrs. Patterson to stall the formation of an interim government and give Mr. Morsi a shot at returning to office.

The Nour Party, which sided with the military and liberal opposition groups in toppling the Morsi government, delayed the appointment of the interim prime minister this week by rejecting the choice of Mohamed ElBaradei, a former chief of the U.N. nuclear watchdog, for the job.

“People saw the U.S. ambassador as somehow trying to pull the strings to bring Morsi back to power,” Mr. Sabry said.

White House spokesman Jay Carney on Wednesday defended Mrs. Patterson as a “supremely skilled diplomat.” He said she continues to enjoy Mr. Obama’s full confidence.

“She’s doing a great job,” Mr. Carney said.

“The suggestion that an ambassador to a country, by engaging with the government, is somehow picking sides misunderstands the function that ambassadors serve,” he said. “Of course Ambassador Patterson engaged with the Egyptian government that was led by President Morsi. That’s part of her job. And she is engaging with the authorities in power now, and she’ll engage with what we hope will be the next democratically elected civilian government when that government’s in place.”

The State Department did not respond to a question about Mrs. Patterson’s reported meeting with the Nour Party.

The Obama administration’s embrace of Mr. Morsi appeared to have loosened in the months preceding the uprising as frustration built in Washington about his inability to work with the opposition and address pressing issues such as the economy and security.

Secretary of State John F. Kerry visited Cairo in March and made the case that the Morsi administration needed to be more inclusive. That argument fell on deaf ears.

Crackdown continues

Egyptian prosecutors on Wednesday ordered the arrests of senior Muslim Brotherhood leaders in a widening crackdown on Islamists.

The arrest warrants for the Muslim Brotherhood’s Supreme Guide Mohamed Badei and nine other Islamist figures charge them with inciting violence in Cairo on Monday in which 51 people were killed and more than 300 injured.

Gehad El-Haddad, a spokesman for the Muslim Brotherhood, said that issuing the warrants is a “political tactic” aimed at disrupting the vigil by thousands of anti-Morsi supporters in Cairo’s Nasr City district.

“It is the same tactics used under [former President Hosni] Mubarak’s police state to create a story they can sell to the public by tying it to a massacre they themselves created,” Mr. El-Haddad said in a phone interview. “They want to try and disconnect the leaders of the protest.”

No Muslim Brotherhood leaders have been taken into custody, but two were missing Wednesday night, Mr. El-Haddad said. He declined to identify them.

The Muslim Brotherhood’s political arm, the Freedom and Justice Party, said the army had fired on “peaceful protesters” who were performing dawn prayers. The military blamed “an armed terrorist group” for instigating the crackdown by first attacking the Republican Guard headquarters, where Mr. Morsi is thought to be under arrest.

The Freedom and Justice Party then called for a “peaceful uprising” against the Egyptian military.

Neither the Muslim Brotherhood nor the military appears willing to back down.

“From [the Brotherhood‘s] perspective, they have been cheated out of power and it is going to be nearly impossible to find the formula to incorporate them into a new process, which is why, I suspect, the military will try to destroy them,” said Eric Trager, an Egypt analyst at the Washington Institute for Near East Policy.

Egyptian media reported that Hazem el-Biblawi, who was appointed interim prime minister Tuesday, will offer the Muslim Brotherhood positions in his Cabinet.

Mr. El-Haddad, the Muslim Brotherhood spokesman, said his party would never accept such an offer.

“We would rather go back to our grass-roots social work,” he said. “[Mr. Morsi] should be reinstated. The votes have to be respected, not the military might.”

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