Story highlights Protesters pelt Clinton's motorcade with tomatoes and shoes

Clinton was not hit, but an Egyptian official was

Clinton discusses Egypt's political transition with the head of Egypt's military leadership

A day earlier, she met President Morsy and urged him to assert his authority

Egyptian protesters threw tomatoes and shoes at U.S. Secretary of State Hillary Clinton's motorcade Sunday and shouted, "Monica, Monica, Monica" as she left the newly reopened U.S. Consulate in Alexandria.

Clinton said she was in the city to answer critics who believe Washington has taken sides in Egyptian politics. There were already vocal protesters at the start of her visit to the consulate, forcing the ceremony to be moved inside.

"I want to be clear that the United States is not in the business, in Egypt, of choosing winners and losers, even if we could, which, of course, we cannot," Clinton said at the ceremony to reopen the consulate, which was closed in 1993 because of budget constraints.

"I have come to Alexandria to reaffirm the strong support of the United States for the Egyptian people and for their democratic future."

The protesters threw the tomatoes, shoes and a water bottle as the staff walked to their vans after the ceremony and riot police had to hold back the crowd. A tomato hit an Egyptian official in the face.

Clinton's van was around the corner from the protesters, and a senior State Department official said her car was not hit.

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The chants of "Monica" refer to Monica Lewinsky, the White House intern who had an affair with Clinton's husband, former President Bill Clinton.

Earlier Sunday, Clinton held a closed-door meeting with the head of Egypt's military leadership, Field Marshal Mohamed Hussein Tantawi, whose military council is in a political tug of war with new President Mohamed Morsy.

Egypt's military leaders took control of the government after a popular uprising toppled former President Hosni Mubarak in February 2011, promising to hand over control after elections.

But after this year's elections, the military council issued a decree stripping the presidency of much of its power. And more than two weeks after Morsy took office, the country remains in the throes of domestic political chaos. The president has no Cabinet and the country has no parliament.

Clinton met with Morsy on Saturday and urged him to assert the "full authority" of his office. She stressed that it is up to the Egyptian people to shape the country's political future, but also said the United States would work "to support the military's return to a purely national security role."

Clinton and Tantawi, who met for just over an hour Sunday, discussed the political transition and the military ruling council's ongoing dialogue with Morsy, said a senior State Department official, who described the meeting on condition of anonymity.

Field Marshal Mohamed Tantawi greets U.S. Secretary of State Hillary Clinton before a meeting in Cairo.

Later Sunday, in meetings with representatives from civil society groups and Christian leaders, Clinton addressed concerns from some who have been skeptical of the United States' neutrality in Egypt's political transition, another senior State Department official said.

"There has been some suspicion, some assertion, and we heard some of that today, that somehow the U.S. has put its finger on the scale in favor of one side or another in this transition," the official said. "And she wanted in very, very clear terms, particularly with the Christian group this morning, to dispel that notion and to make clear that only Egyptians can choose their leaders, that we have not supported any candidate, any party, and we will not."

As she left the country Sunday night, Clinton said her two days of meetings showed her the Egyptian people "have legitimate concerns, and I will be honest and say they have legitimate fears about their future."

Egypt's fragile economy has been a top item on Clinton's agenda during the trip. The secretary of state also met with business entrepreneurs affiliated with Flat6Labs, an organization that provides seed money, mentoring and work space to small Egyptian companies to help them realize their concepts.

"Thanks to all of you for being willing to take a risk," she said.

Clinton aides said the secretary of state wanted to visit Cairo early after Morsy's swearing-in to show that the Obama administration wants to help the new government improve Egypt's economy.

In meetings with Morsy and Tantawi, Clinton discussed a U.S. economic package that would relieve as much as $1 billion in Egyptian debt and help foster innovation, growth and job creation, officials said. She also said the United States is ready to make available $250 million in loan guarantees to Egyptian businesses.

Tantawi told Clinton that what Egyptians need most now is help getting the economy back on track, one senior State Department official said.

Egypt's military is the foundation of the modern state, having overthrown the country's monarchy in 1952. Tantawi, a 76-year-old career infantry officer, fought in Egypt's 1956, 1967 and 1973 wars with Israel.

The Supreme Council of the Armed Forces, which Tantawi heads, currently wields legislative power, having ordered the dissolution of parliament after the country's highest court ruled that it had been elected under invalid laws.

Morsy tried to call it back into session after he was sworn in, but the court reaffirmed its decision, so the military council retains lawmaking powers until a new parliament is sworn in near the end of the year.

In the presidential election, Morsy edged out Ahmed Shafik -- the last prime minister under Mubarak -- winning nearly 52% of the votes cast.

He resigned from the Muslim Brotherhood and its Freedom and Justice Party shortly after the results were announced, in an apparent effort to send a message that he will represent all Egyptians.