Hillary Clinton meets Egypt military leader Tantawi
US Secretary of State Hillary Clinton has met the head of Egypt's top military council, Field Marshal Mohamad Hussein Tantawi, on the second day of her visit to the country.
Mrs Clinton discussed the transition of power to newly elected President Mohammed Mursi and stressed the need to protect the rights of all Egyptians, US officials said.
Mrs Clinton met Mr Mursi on Saturday.
Mr Mursi and the military have been in conflict over parliament's dissolution.
The Supreme Council of the Armed Forces (Scaf) shut down the chamber, dominated by Mr Mursi's Islamist allies, before he was formally sworn in last month.
It also stripped the new president, elected in the country's first freely contested leadership vote earlier in June, of many of his powers.
Mr Mursi, of the Muslim Brotherhood's Freedom and Justice Party, tried to reinstate parliament by decree last weekend. The Supreme Constitutional Court has said the dissolution is final.
As head of the Scaf, Field Marshal Tantawi became Egypt's interim ruler after the fall of President Hosni Mubarak in February last year.
Mrs Clinton held talks for more than an hour on Sunday with Field Marshal Tantawi.
A senior US state department official said: "They discussed the political transition and the [military council's] ongoing dialogue with President Mursi.
"The secretary stressed the importance of protecting the rights of all Egyptians, including women and minorities."
Field Marshal Tantawi brought up Egypt's economic needs, while the pair also discussed US aid plans.
After meeting Field Marshal Tantawi and other army leaders, Mrs Clinton headed to Egypt's second city, Alexandria, a stronghold of the Muslim Brotherhood.
Protesters in the city targeted her motorcade, with shoes, water bottles and tomatoes thrown towards the armoured vehicles.
A senior state department official said that neither Mrs Clinton or her vehicle were struck by any of the objects thrown.
Speaking at the newly re-opened US consulate in Alexandria, Mrs Clinton said: "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."
She added: "Democracy is not just about reflecting the will of the majority. It is also about protecting the rights of the minority."
Mrs Clinton also held meetings with leading women, the Coptic Christian community and young entrepreneurs.
On Saturday, Mrs Clinton told Mr Mursi that the situation required "compromise and real politics".
She praised Egypt's military council for its interim leadership, "for representing the Egyptian people in the revolution as compared to what we are seeing in Syria which is the military murdering their own people".
But she also voiced support for a "full transition to civilian rule".
The secretary of state also encouraged President Mursi to live up to promises to protect the rights of women and minorities, and to preserve the peace treaty with Israel.
The hour-long meeting between President Mursi and Mrs Clinton was described by a US official as candid and cordial.
However, on Saturday evening hundreds of demonstrators gathered outside Mrs Clinton's Cairo hotel, chanting anti-Islamist and anti-US slogans in protest at her visit. Some brandished posters depicting the field marshal.
Another protest outside the US embassy was organised by Coptic Christian youth activists, who chanted: "They both can't be trusted, not the Americans, not the Brotherhood."
The BBC's Jon Leyne, in Cairo, says that for all the US fears of an Islamist takeover in recent decades, the governments in Washington and Egypt have now realised they need each other.
Mr Mursi and the Muslim Brotherhood are particularly keen to avoid the sort of international isolation so damaging to other Islamist governments after they have taken office, our correspondent adds.
The Secretary of State has now flown to neighbouring Israel for talks with political leaders there.