As a student at the National War College in Washington, the chief of staff of Egypt’s armed forces argued in a paper that the American military presence in the Middle East and its “one-sided” support of Israel were fueling hatred toward the United States and miring it in an unwinnable global war with Islamist militants.

The paper, written seven years ago by Gen. Sedky Sobhi, offers an early and expansive look into the thinking of one member of the new generation of military officers stepping into power as part of a leadership shake-up under Egypt’s newly elected president, Mohamed Morsi of the Muslim Brotherhood.

His sharp rebuke of American policy is especially striking because he now oversees the military institution that has been the closest United States ally in the Arab world, relied on by American officials as a critical bulwark in support of Israeli security and against Iranian influence. Despite decades of military collaboration, he urged a full pullout of American forces from the region.

Scholars say his paper is even more significant in part because many of its themes reflect opinions widely held by Egyptians, their new president and people throughout the region — an increasingly potent factor in regional foreign policy, as Egypt and other countries struggle toward democracy.

American officials said their confidence in Egypt was unshaken, while analysts argued that despite the changes in the nation’s military and civilian leadership, any realignment in relations with Washington could be slow — in part because of Egypt’s urgent need for assistance from the United States and the West.

“For sure there are going to be big changes in Egypt’s relationship with Washington,” said Shibley Telhami, a political scientist at the University of Maryland and a scholar at the Brookings Institution who has studied Arab and Egyptian public opinion.

In surveys across the Arab world for more than a decade, he said, about 70 percent of the public has named the United States as the second greatest threat to regional security, after Israel — even in Egypt, where Washington provides $1.3 billion in annual military aid, and in Saudi Arabia, another close American ally.

As General Sobhi argued, Professor Telhami said, “there were always two central issues driving Arab and Egyptian anger with the U.S., the Palestinian question — the prism of pain through which Arabs see the West — and the U.S. military presence.”

General Sobhi’s paper, first reported by the Cairo independent journalist Issandr El Amrani, offers a rare look into the foreign policy thinking of a military institution often considered all but impenetrable to outsiders.

For decades under President Hosni Mubarak, the Egyptian military, and the nation’s foreign policy, had been closely allied with the United States and its regional interests. There was concern in Washington after Mr. Mubarak’s ouster that the relationship might not survive — an anxiety that was revived when Mr. Morsi was elected president.

But Washington knew that the longtime defense minister, Field Marshal Mohamed Hussein Tantawi, and his chief of staff, Sami Hafez Anan, still wielded considerable power and were reliable allies.

Then after an embarrassing terrorist attack in northern Sinai this month, Mr. Morsi appeared to consolidate his power by announcing their replacement, while keeping them on as presidential advisers. The shake-up raised for the first time the possibility that Mr. Morsi might begin to exert some real sway over Egyptian foreign policy, and General Sobhi’s paper suggested that at least some of the younger cadre of generals might share an interest in more independence from Washington.

In his paper, General Sobhi spells out a position that fits well with the campaign vows of many Islamist and secular politicians in Egypt to chart a course more independent of Washington. “If the relationship is between equals, with mutual respect and mutual interest, then nothing changes,” Mahmoud Hussein, the secretary general of the Muslim Brotherhood, said this week of the Egyptian relationship with the United States. “But if the U.S. thinks the relationship with Egypt is of a master and a follower, then this will never be.”

Samer Shehata, a professor of Arab politics at Georgetown University, said that American policy makers would be naïve to think that the positions held by Mr. Morsi and the Brotherhood — including criticisms of the United States and strong support for the Palestinians — represented fringe thinking.

On those issues, “the Brotherhood is the Egyptian Kansas,” said Professor Shehata. Their positions on foreign policy “reflect rather than oppose what the Egyptian center is thinking,” he said.

In Washington, officials said they were unconcerned about the paper or the broader changes in the leadership of the Egyptian military. Top United States defense officials have said that they enjoy strong and positive relationships with General Sobhi and his boss, the new defense minister, Gen. Abdul Fattah el-Sisi, who also studied at the National War College in Washington.

“A lot of academic theses offer up interesting ideas that don’t go very far, and often end up as shelf ware,” a senior official in the Obama administration said of General Sobhi’s paper, speaking on condition of anonymity because of the delicate point in relations with Egypt. “This isn’t exactly causing concern. We believe we will work well with the new Egyptian military leaders.”

Other analysts, though, argue that the defense shake-up, which signaled an apparent consolidation of Mr. Morsi’s power, inevitably augured a larger shake-up ahead for Egyptian relations with Washington.

Given the pressure of public opinion on democratically elected leaders — to say nothing of the Brotherhood and Mr. Morsi’s history of criticizing the United States’ Middle East policy — “it thus stands to reason that Morsi’s sacking of Egypt’s top national security and defense officials might in part represent a shift in Egyptian foreign policy away from the United States,” the scholar Steven A. Cook argued this week on the Web site of the journal Foreign Affairs. “Toward what country, however, remains unclear. There is no other power that could be Egypt’s patron, yet Cairo might not need one. Egypt, representing a quarter of the Arab world and strategically located on the Suez Canal and Afro-Asian rift — is a power in its own right.”

General Sobhi couched his paper as an argument to American policy makers about their long-term interest.

But he made his case by focusing on what he said were American misunderstandings of the region, arguing that Westerners undermined their professed support for Arab democracy with their hostility toward the role of Islamic law in many Arab states. The push for democracy “must have and project political, social, cultural and religious legitimacy,” he wrote.

General Sobhi also argued that it was wrong to characterize Al Qaeda and other militant groups as merely “irrational terrorist organizations.” Instead, he suggested that they had tapped into popular grievances with American policy, “becoming an international insurgency movement.”

“I recommend that the permanent withdrawal of United States military forces from the Middle East and the Gulf should be a goal of U.S. strategy in this region,” he wrote, adding that the United States should pursue its objectives through “socioeconomic means and the impartial application of international law.”

David D. Kirkpatrick reported from London, and Kareem Fahim from Cairo. Steven Lee Myers contributed reporting from Washington, and Elisabeth Bumiller from Fort Campbell, Ky. (Copyright 2012 The New York Times Company 08/17/12)