Egypt's military is aplogizing for the deaths of at least 35 protesters in a series of clashes with police this week.

The apology was issued as a fragile truce took hold in Cairo's Tahrir Square, which had been a flashpoint for the violent skirmishes between police and protesters calling for the country's miltary rulers to step down immediately.

Army troops used metal bars and barbed wire to separate protesters and police along a street that has seen some of the most intense clashes. Meanwhile, the statement from the country's military rulers promised to bring those responsible for the death to justice.

The latest clashes erupted early Thursday east of Cairo, in Ismailia, a city along Egypt's Suez Canal. Some protesters hurled Molotov cocktails at troops who moved through the streets in armored vehicles and tanks to the steady sound of gunfire.

Some protesters accused the military of more unprovoked violence.

In the coastal city of Alexandria late Wednesday, protesters set up barricades and hurled stones at police. Others held hands in front of military buildings and chanted “freedom.”

U.N. High Commissioner for Human Rights Navi Pillay on Wednesday urged Egyptian authorities to end what she called “clearly excessive force against protesters” called images of the brutal beatings of subdued protesters “deeply shocking.”

Field Marshal Hussein Tantawi, the head of the Supreme Council of the Armed Forces, has pledged to speed the transition to civilian rule with presidential elections before July 2012.

Parliamentary elections are set to begin on Monday and Tantawi pledged the polls would go forward as planned. But many opposition leaders believe that to be increasingly doubtful.

Meanwhile, Egyptian authorities said Wednesday three American students arrested during protests in Cairo earlier this week are being questioned by local police in the presence of a lawyer and a U.S. embassy official.

Egyptian media report that the three, all students at American University in Cairo, were detained along with other protesters while throwing petrol bombs at police.

No formal charges have been brought against the students, who insisted they did nothing wrong.