CAIRO — US Secretary of State Hillary Clinton met Sunday with Egypt's top military leaders, urging them to support a transition to civilian rule as a political struggle triggers fears that rights could be eroded.

On the second and final day of her visit to Egypt, the top US diplomat also met with representatives of the country's 10 million-strong Christian community, saying afterwards Washington was "committed to protecting and advancing the rights of all Egyptians: men and women, Muslim and Christian."

Clinton's trip to Egypt comes at a time when a complex power struggle is being played out between the newly elected Islamist president, Mohamed Morsi, and the Supreme Council of the Armed Forces (SCAF).

After meeting Morsi soon after arriving in Cairo on Saturday, Clinton on Sunday spent more than an hour in talks with Field Marshal Hussein Tantawi — the country's interim military ruler after president Hosni Mubarak was ousted last year.

"They discussed the political transition and the SCAF's ongoing dialogue with President Morsi," a state department official told reporters at the end of the talks.

The two also discussed an economic package proposed by Clinton and "Tantawi stressed that this is what Egyptians need most now, help getting the economy back on track," the official said.

Clinton has repeatedly called on the military to respect the outcome of the elections and told a news conference on Saturday that her talks with Tantawi would focus on "working to support the military's return to a purely national security role."

Morsi, Egypt's first democratically elected president, is locked in a standoff with the military after he ordered parliament to reconvene, defying an army decision to disband the house.

But a declaration issued by the SCAF before Morsi was sworn in — which acts as a temporary constitution — granted the military sweeping powers, including legislative control, even though they handed over to Morsi on June 30.

While Morsi's decree was applauded by supporters, it set off a firestorm of criticism from opponents who accused him of overstepping his authority.

Choosing her words carefully in the politically-charged atmosphere, Clinton said "it is very clear that Egyptians are in the midst of complex negotiations about the transition" including the make-up of parliament, a new constitution and the full powers of the president."

"Democracy is hard," she said. "It requires dialogue and compromise and real politics. We are encouraged and we want to be helpful. But we know that it is not for the United States to decide, it is for the Egyptian people to decide."

Hundreds of protesters had gathered outside the US embassy and later Clinton's hotel to denounce what they said was "US interference in domestic affairs", the official MENA news agency reported.

The US and Egyptian militaries have had a 30-year close alliance, and at the chaotic news conference one Egyptian reporter repeatedly tried to ask Clinton why the US had resumed its $1.3 billion in annual military aid.

A senior state department official said Clinton would "encourage Tantawi... to engage in dialogue and to avoid the kind of confrontation that could potentially lead to the transition veering off track."

Clinton's meeting with Christian leaders comes after women and religious minorities expressed fears their rights could be rolled back following the post-revolution rise of the Islamists.

"I came to Cairo, in part, to send a very clear message that the United States supports the rights, the universal rights of all people," Clinton said.

"We are going to look to any elected government to support inclusivity, to make sure that the talents of every Egyptian can be put to work in building a new future for this ancient and incredibly important country," she said.

Egypt's Christians have long complained of discrimination and marginalisation even under Mubarak's secular regime.

The election of an Islamist president has raised fears of further discrimination of the community, many of whom had backed Morsi's rival, Ahmed Shafiq — Mubarak's last prime minister — in the landmark presidential polls.

Some Christian and secular activists had accused the United States of siding with Morsi during the election.

"There has been... some suspicion, some assertion, and we heard some of that today... that somehow the US has put its finger on the scale in favour of one side or another in this transition," a state department official told reporters.

But Clinton "wanted in very, very clear terms... 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," the official said.