CAIRO — Secretary of State Hillary Clinton arrived in Egypt on Saturday for meetings with its newly elected Islamist president and the chief of its still-dominant military council, declaring that the United States “supports the full transition to civilian rule with all that entails.”

But after weeks of internal debate across the Obama administration over how to respond to the ongoing struggle between the president and the generals, Clinton touched on it only lightly, saying she looked forward to working “to support the military’s return to a purely national security role.”

State Department officials said the meeting itself sent a historic message. Seated in an ornate room in the presidential palace, Clinton smiled for cameras and traded pleasantries with President Mohammed Morsi of the Muslim Brotherhood, an Islamist jailed more than once by the U.S.-backed autocracy overthrown 18 months ago. She became the highest ranking U.S. official to meet Morsi since he was sworn in two weeks ago as Egypt’s first democratically elected president.

But her outreach to the new president appeared constrained by evident reluctance to address his struggle to pry power from the generals. In brief remarks after the meeting with Morsi, her sole reference to the military decrees dissolving the Islamist-led Parliament and eviscerating his powers was a call for “consensus” among all sides in order “to work on a new constitution and Parliament, to protect civil society, to draft a new constitution.”

Clinton’s tone appeared softer than that of State Department comments made only a few weeks ago, when the military council had moved to disband Parliament on the eve of the presidential race. At the time, a State Department spokeswoman publicly urged the generals to meet their “commitments to the Egyptian people.”

Along with their core strategic concerns about maintaining a stable ally in Cairo and preserving the peace with Israel, State Department officials say, they continue to hope that Egypt will move toward a more democratic and fully civilian form of government. But at the moment, U.S. policy is beset from all sides.