The truce lasted about three hours.
CNN saw military police lined up, separating protesters from the police.
But after a period of calm, some protesters began throwing rocks at soldiers. Riot police responded with tear gas; the unrest continued late Wednesday.
Some army soldiers tried to stop security forces from shooting tear gas, but they were outnumbered.
On state-run TV, the government said religious scholars were on their way "to form a human shield between the protesters and the security forces."
CNN saw no sign of a human shield of clerics. But along the barricades separating protesters from security forces, some clerics were talking to protesters, trying to negotiate.
Egypt's grand mufti, the country's highest religious official, called on police to put down their weapons and "never aim" firearms at the Egyptian people. In an audio message aired by Egyptian state TV, he called for a "peaceful protest for Egypt's sake."
Protesters reached Fahmi Street, which leads to the Interior Ministry, and were trying to surround the ministry, state-run Al-Masriya TV said.
Earlier, police pulled back from Mohamed Mahmoud Street, the site of clashes throughout the five days of the latest uprising.
Adel Saeed, spokesman for the Egyptian general prosecutor's office, said "a truce has been reached between the protesters and the security forces at the Ministry of Interior through several leading religious scholars."
It was not immediately clear who may have been represented in the discussions to which Saeed referred.
Mohamed Mahmoud Street leads from Tahrir Square -- the center of the protests that toppled Hosni Mubarak as president in February and of the most recent demonstrations -- toward the Interior Ministry.
During a lull in the street battles earlier Wednesday, CNN saw riot police embracing and kissing some young people who were taking part in the demonstrations. Minutes later, rocks and tear gas were in the air again.
Protesters erected barriers using debris from burned-out cars and large trash bins in case the battles resumed.
Crowds have packed Tahrir Square since Saturday, calling for the nation's military rulers to step down immediately. The demonstrations Wednesday were a vociferous rejection of Mohamed Hussein Tantawi, field marshal of the Supreme Council of the Armed Forces, who delivered an address Tuesday aimed at calming the protests.
"The people demand the downfall of the council of shame," some demonstrators chanted Wednesday.
Through the state-run news agency MENA, the government said that the army was "exerting all efforts to stop bloodshed of Egyptians" and that the military had deployed three armored vehicles to Mohamed Mahmoud Street.
The death toll in the latest clashes has risen to 35, including 31 people in Cairo and four in other cities, state-run television said Wednesday.
The number of wounded is up to 3,250, according to Hisham Sheeha, spokesman for Egypt's Health Ministry.
Saeed, of the Egyptian general prosecutor's office, said 312 people had been arrested since Saturday.
Security forces could be seen making arrests Wednesday. Egyptian-American filmmaker Jehane Noujaim was among those arrested, according to Karim Amer, a film producer who said he was with her when she was filming events close to the Interior Ministry.
"The military started firing tear gas so we all ran in different directions and I lost her," Amer said. "She called me and said she was arrested by military. " A CNN e-mail to noujaimfilms.com, which lists Noujaim as director, was not immediately returned.
Meanwhile, the mother of one of the three American students detained in Egypt said Wednesday that she was able to speak to him briefly in a telephone call arranged by U.S. diplomats.
"He sounded scared, but he said he was OK," Joy Sweeney said of her son, Derrik Sweeney, one of three American college students being held for questioning in an Egyptian courthouse, accused by authorities of throwing Molotov cocktails in Tahrir Square.
The students will be detained another four days as an investigation continues, said a spokesman for the office of Egypt's general prosecutor.
An official from the U.S. consular office visited the students, said U.S. Embassy spokeswoman Katharina Gollner-Sweet.
The chaos and fighting have raised new questions about Egypt's future less than a week before parliamentary elections are set to begin.
U.N. High Commissioner for Human Rights Navi Pillay called on Egypt "to end the clearly excessive use of force."
"Some of the images coming out of Tahrir, including the brutal beating of already subdued protesters, are deeply shocking, as are the reports of unarmed protesters being shot in the head," Pillay said in a statement. "There should be a prompt, impartial and independent investigation, and accountability for those found responsible for the abuses that have taken place should be ensured."
After Mubarak's ouster, military leaders took control with the promise that eventually a civilian government would be elected and take over.
Demonstrators say they are concerned the military, which would continue to be Egypt's top authority until a president is in place, wants to keep a grip on the country.
Many also have voiced anger about a proposed constitutional change that would shield the military's budget from scrutiny by civilian powers. They say they worry the military would become a state within a state.
Members of the nation's Cabinet offered to resign Monday, with one minister citing concern over the violence in Tahrir Square.
Tantawi of the Supreme Council of the Armed Forces said the resignations were accepted, but the current government will remain as a caretaker until a prime minister is named to form a new government.
Speaking Tuesday on Egyptian TV, Tantawi said the armed forces were "only concerned about the security of the country and the interests of the country," and want to "establish democracy for the people of Egypt."
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