Before Secretary of State John Kerry’s recent trip to Cairo, National Security Adviser Susan Rice told him to make strong statements in public and private about the trial of deposed President Mohamed Morsi. On his own, Kerry decided to disregard the White House’s instructions.

The tension between the national security adviser and the secretary of state spilled over into public view in the past week, when Rice laid out her critical appraisal of the Egyptian government, which contradicted Kerry’s assessment that Egypt was “on the path to democracy.” The now public rift has been simmering behind the scenes for months and illustrates the strikingly divergent Egypt policies the White House and the State Department are pursuing.

The turf battles and internal confusion are hampering the administration’s approach to Egypt, say lawmakers, experts, and officials inside both governments.

“John Kerry doesn’t agree with Susan Rice on big portions of our Egypt policy, and he made a deliberate and conscious decision not to mention Morsi in his Cairo meetings,” an administration official told The Daily Beast. “Susan Rice wasn’t happy about it.”

Two other administration officials confirmed the Kerry-Rice rift over Egypt. The secretary and national security adviser’s disagreement about how to handle the tumultuous and troubled U.S.-Egypt relationship is only the latest example of how the White House has steered America’s approach to Egypt in a way that conflicts with the views and desires of the State Department and the Pentagon, said the two officials.

“The roadmap [to democracy] is being carried out to the best of our perception,” Kerry said November 3 at a press conference during his surprise stop in Cairo, standing alongside the Egyptian foreign minister. “There are questions we have here and there about one thing or another, but Foreign Minister Fahmy has reemphasized to me again and again that they have every intent and they are determined to fulfill that particular decision and that track,” he said.

Never once during his trip did Kerry publicly mention Morsi, whose trial on charges of murder and other alleged crimes began November 4. Administration officials and sources close to the Egyptian government said Kerry also did not raise the Morsi trial in his various private meetings with Egyptian officials.

Rice delivered less praise and more admonishment for the Egyptian government in remarks at The Aspen Institute’s Washington Ideas Forum on November 13.

“We have tried to indicate to the Egyptian people and the Egyptian government that we support them in their transition back to an elected democratic government,” she said. “But that government needs to be inclusive. It needs to be brought about through a process in which all Egyptians can participate, and without violence. So when, in August, in the process of trying to clear the protesters from some of the squares in Cairo, over 1,000 people were killed, the United States, I think quite rightly, said, you know, ‘We have a problem with that. And we can’t pretend to conduct business as usual on the context of a government, however friendly, taking that kind of action against its people.’”

Well before Kerry and Rice disagreed publicly on Egypt, the White House and the State Department clashed privately over the administration’s Egypt policy. During a months-long administration review of U.S. military aid to Egypt, the State Department and Defense Department pushed internally to preserve most of the assistance, while the White House insisted most military aid be suspended, pending more progress by the Egyptian government.

“There are real differences in the fundamental approach to Egypt between Susan Rice and John Kerry,” said one Washington Egypt expert with close ties to the administration. “We wouldn’t have had any aid suspension at all if it had been up to John Kerry and Chuck Hagel.”

Rice, who has spent the bulk of her career dealing with Africa, has a long record of emphasizing human rights and democracy concerns. Kerry leans more toward economic diplomacy and engagement with regimes who may not be on their best behavior. Hagel has close relationships with Egypt’s military leaders and has spoken to Gen. Abdel Fattah al-Sisi more than 20 times since the overthrow of the Morsi government.

But several officials also said the rift stems from the State Department’s institutional bias toward working with governments in power and maintaining important relationships. In Cairo, Kerry followed the recommendation of his own bureaucracy, which was not to mention Morsi’s name. The U.S. Embassy in Cairo, concerned about its own security since the attacks of Sept. 11, 2012, also is wary of making strong statements about the Morsi trial.

The White House maintains that all parts of the Obama administration share the same overall goal: to help Egypt get back on track toward being a functional democracy operating under the rule of law.

“The entire national security team—including Ambassador Rice, Secretary Kerry, and Secretary Hagel—is working in lock step to implement the president’s policy on Egypt: namely, to encourage Egypt’s transition to an inclusive, democratically elected, civilian-led government that respects the rights and freedoms of all Egyptians,” Patrick Ventrell, a spokesman for Rice, told The Daily Beast. “The current interim government has laid out a clear roadmap for Egypt’s return to democratic rule, and across the administration we are working with Egypt’s leaders to strongly encourage them to meet their commitments.”

A senior State Department official told The Daily Beast that Kerry often raised the issue of the Egyptian government’s crackdown on the Muslim Brotherhood during his trip, even if he didn’t utter Morsi’s name.

“[Kerry] repeatedly pressed the interim government on politically motivated and arbitrary detentions, arrests, and trials in every meeting he had,” the official said. “He also used the word ‘inclusive’ about a dozen times per meeting, stressing that the Muslim Brotherhood needed to be a part of the process.”

Nevertheless, officials and experts said the administration’s Egypt policy is hampered not only by internal tensions but also by being ad hoc and reactive, without a long-term strategy dictated by President Obama.

“What’s missing from any of the administration’s statements or actions is a clear vision of how they will preserve American interests in Egypt over the long term,” said Tamara Cofman Wittes, director of the Brookings Institution’s Saban Center and a former State Department official. “The president clearly made an analytical judgment that authoritarianism in the Middle East was not stable in the long term. If he still believes that, then he has to have some concerns about Egypt’s trajectory and American interests, and how to address those concerns is missing from American policy today.”

In Egypt, officials are receiving diverging messages from the U.S. government’s various parts, causing confusion as they try to decide how to react to recent U.S. actions. For example, the administration has not told the government of Egypt what exactly it must do to get the partial aid suspension lifted, said a source close to the Egyptian government.

“They are getting different messages from different people in Washington. There is confusion in Egypt as to what is actually U.S. policy,” the source said. “There is a vagueness and an unclear policy.”

Meanwhile, on Capitol Hill, the administration is lobbying Congress to pass legislation that would allow for some military aid to Egypt to continue, but the effort is faltering. Lawmakers in both parties are still upset the administration refuses to make a determination that the Morsi overthrow was a coup.

The administration is following a law that would restrict military aid for any country that has a coup, despite its reluctance to use that word. A bill to give the administration specific authorities to continue some aid was pulled from the agenda of the Senate Foreign Relations Committee business meeting last week because various senators could not agree on what restrictions they should put on the administration’s ability to disperse the aid.

Sen. Lindsey Graham (R-SC), the ranking Republican on the Senate Appropriations State and Foreign Ops subcommittee, told The Daily Beast in an interview that he is opposed to giving the government of Egypt any more aid until it takes major steps toward restoring the rule of law.

“I’m not going to authorize more assistance to Egypt until they march toward a transition to a civilian-controlled government,” he said. “My goal is to not reinforce the coup but to reinforce the transition.”

Asked about the Kerry-Rice split on Egy pt policy, Graham said, “I’m in the Susan Rice camp.”