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“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.

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