CAIRO — Mohamed Morsi of the Muslim Brotherhood was formally sworn in on Saturday as the first democratically elected president of Egypt, signaling a new stage in an ever murkier struggle to define the future of the nation after six decades of military-backed autocracy.

Proclaiming “a new Egypt, the second republic,” Mr. Morsi declared, “Today the Egyptian people have established a new life, with real freedom and real democracy.”

More immediately, though, his inauguration begins a through-the- looking-glass period of government at war with itself. As Egypt’s first civilian president and the first Islamist elected to lead an Arab state, Mr. Morsi has vowed to fulfill the goals of the Egyptian revolution by building the institutions of democracy on a foundation of Islamic principles.

But he must first wrest power from the generals who have ruled Egypt since the ouster of President Hosni Mubarak. Although they trumpeted their handover on Saturday, they have taken only a small step behind the scenes to accommodate Mr. Morsi’s election.

His swearing-in ceremony itself was redolent with tension. Mr. Morsi, against his wishes, took the oath before a court of Mubarak-appointed judges; he had vowed to swear in before the democratically elected and Islamist-led Parliament, but the generals dissolved it on the eve of his election under the pretext of a ruling from the very same court.

Seated in the curved alcove at the front of an empty courtroom, Mr. Morsi frowned and stared ahead as senior judges stood to deliver speeches as much about the importance of their own Supreme Constitutional Court as about his historic inauguration.

“We welcome you in this Supreme Constitutional Court and we appreciate your presence here today in this great judicial institution,” said Farouk Sultan, the president of the court. “Your physical presence here today is a real symbol of support for constitutional legitimacy and upholding the law over everyone.”

In inviting the new president to take the oath, Judge Sultan specifically cited the authority of the interim Constitution issued by military decree on June 17, which transferred most of the powers of the president’s office to the ruling generals — a document Mr. Morsi, the Brotherhood and thousands of demonstrators occupying Tahrir Square have called illegitimate.

In his own briefer remarks after taking the oath at the court, Mr. Morsi pushed back with a jab at the judges’ role in the dissolution of Parliament, referring repeatedly to the separation of powers. “I respect the judiciary and the legislature and I will work to keep them independent from each other and from presidential power,” he said. “The judicial power, the executive power, the legislative power — we will all go forward together.”

Mr. Morsi pre-empted the generals’ planned inauguration by reciting his oath a day earlier in a televised speech before a rapturous crowd that filled Tahrir Square, the heart of the revolution. And on Saturday, Mr. Morsi proceeded to recite the same oath a third time, in a Cairo University auditorium packed with lawmakers of the dissolved Parliament, the ruling generals and foreign ambassadors.

Field Marshal Mohamed Hussein Tantawi, who had acted as head of state until Saturday and will maintain the title of defense minister by military fiat, sat at the center of the front row.

“Egypt will not go backward,” Mr. Morsi said. “In the new Egypt, the president will be an employee, a servant to the people.”

But he also continued his unmistakable efforts to wield the prestige of his new post against the ruling generals. Without acknowledging the dissolution of the legislature, he praised the Parliament as a triumph of democracy. “The people projected their will and exercised their power with the election of Parliament in free and fair elections representative of society,” he said. He dedicated a “big salute” to the ruling Supreme Council of the Armed Forces for its role in safeguarding the transition.

But he also pointedly called for the military to return to the barracks and borders. “The elected institutions will come back to play their role and the Egyptian armed forces, Egypt’s great army, will go back to its main job to maintain and safeguard the borders,” he said, pledging to keep the armed forces “strong and solid, to work with the other institutions of the government, within the Constitution and within the law.”

In his remarks on Friday, he had avoided any mention of the armed forces, either laudatory or confrontational, in a signal that negotiations between the Brotherhood and the generals continue behind the scenes to resolve the standoff over the balance of powers.

Like almost all Egyptian orators, Mr. Morsi missed no opportunity to invoke God’s oversight. But he never mentioned Islamic law. Its adoption had been a staple of his stump speeches during the first round of Egypt’s presidential elections, when he campaigned against rival Islamists, but he dropped it when he pivoted into the runoff against a more secular opponent.

Addressing the world, Mr. Morsi proclaimed “a message of peace as well as righteousness and justice.” He repeated his pledge to uphold Egypt’s treaty obligations, implicitly including its pact with Israel.

“We are not exporting revolution and we do not interfere with the affairs of others, or allow interference in our own affairs,” he said.

But he also promised with new force that he would work for the reconciliation of the rival Palestinian factions: the Western-backed Fatah, which controls the Palestinian Authority, and the militant Islamist group Hamas, which controls the Gaza Strip. Fatah had previously looked to the Mubarak government as its principal Arab sponsor, while Hamas — an offshoot of the Brotherhood — is increasingly looking for leadership from the new leaders in Cairo.

“I say from here that Egypt is with the Palestinian people,” he said. “We will work for reconciliation until they unite and get their rights.”

And he singled out the uprising in Syria. Backed by the Syrian affiliate of the Muslim Brotherhood, the rebels have lost thousands of lives and been enmeshed in daily battles against the forces of President Bashar al-Assad. “We want this bloodshed to stop and we will work on that,” Mr. Morsi said. “We do not forget the Arab nation.”

In the most theatrical moment of the day, the generals then formally handed over power at a martial ceremony at a parade ground on a nearby base. Field Marshal Tantawi saluted the new president. “We kept our promise,” he said, presenting Mr. Morsi a medal.

Although supporters of Mr. Morsi in Tahrir Square still chant for the end of military rule, he played along and commended Field Marshal Tantawi for submitting voluntarily to the will of the people. “It is a grand day for Egypt,” Mr. Morsi said. Then he posed for a picture surrounded by generals.

In truth, their handover — and with it the Egyptian revolution — remains far from complete. A new constitution is yet to be written and the balance of power between the president and the generals is still undefined, and Mr. Morsi has not yet named a new cabinet. But it appeared Saturday that Mr. Morsi — an engineering professor of modest stature and small charisma — had gained new clout from the trappings of presidency.

He came and went in a Mercedes limousine surrounded by a motorcade and presidential guard. He was greeted at Cairo University by a formal salute from a military color guard. His movements and statements were broadcast attentively by Egyptian state television, whose newscasters had appeared until a few days ago to harbor a bias against him.

The main headline in the flagship state newspaper quoted Mr. Morsi’s speech on Friday: “The people are the source of authority.” Mai Ayyad contributed reporting. (Copyright 2012 The New York Times Company 07/01/12)