Israel released about 550 Palestinian prisoners on Sunday night in the second half of a swap that freed one of its soldiers, Gilad Shalit, who had been held by Hamas in Gaza for more than five years.

The prisoners left Ofer Prison in Israel by bus shortly after 10 p.m., with a dozen buses going to the West Bank and one to Gaza. Some prisoners were also going to East Jerusalem and Jordan.

At the Palestinian presidential compound in Ramallah, music blared and hundreds of Palestinians waved flags, waiting for the buses to arrive. Palestinian youths threw stones at Israeli troops at a checkpoint as the release began.

The soldiers responded with tear gas and rubber bullets. More than a dozen injuries were reported among the Palestinians, and one soldier was hurt.

Sarah Abu Sneineh came with her family to greet her grandson Izzedine Abu Sneineh, who was arrested three years ago at age 15 for weapons training, attempted murder and possession of explosives.

“He was just a schoolkid when he was arrested,” she said as she waited for him outside the tomb of Yasir Arafat. “We want him to go back to school. Only education is the way forward.”

After the buses arrived, escorted by Red Cross jeeps, the freed prisoners went first to Mr. Arafat’s tomb and then to the celebration awaiting them next door. President Mahmoud Abbas of the Palestinian Authority left Sunday for a visit to Turkey, so the reception at the presidential compound was to be brief.

The first phase of the exchange, in which Israel released 1,027 prisoners, took place in October and involved hundreds of Palestinians serving life sentences, many of them Hamas members convicted of killing Israelis.

This second phase involved what the Israelis call light security prisoners. None had been convicted of killing or wounding anyone, and none were members of Hamas or Islamic Jihad.

About half of the prisoners were serving four years or less, and a third of them two years or less, often for offenses like throwing stones or incendiary bombs or possessing weapons. About 10 percent had sentences of 10 years or more, mostly for throwing or planting bombs or attempted murder. Ten percent are younger than 18; three of the prisoners are 14 years old.

Some Palestinians expressed anger that the release took place at night, making it hard to celebrate, and said that those being freed were not the ones they would have chosen.

“This is not a serious part of the exchange,” Issa Qaraqe, the Palestinian minister of detainees for the West Bank-based Palestinian Authority, said in a telephone interview. “Many of those being released were due to get out within months anyway, and there are women left behind and prisoners who have been there a long time. If Israel had wanted to make a real good-will gesture, the list would have been totally different.”

Under the deal, Israel picked the prisoners released in the second group, with the only condition being that they be security prisoners and not those convicted of common crimes.

In Gaza, a spokesman for Hamas, Salah al-Baradweel, said Israel seemed to be punishing Gaza by freeing so few prisoners from there: 41 of the 550. Mid-level Hamas officials were slated to receive the freed detainees. Ihabal Ghussein, spokesman for the Hamas Interior Ministry, said a larger celebration would come later.

Mr. Shalit, who was 19 when he was abducted while on active duty near the Gaza border in 2006, emerged thin and pale when the first phase of the exchange took place. He is now home with his family in northern Israel and undergoing occupational therapy and debriefing by the military, according to Israeli news media reports.

He has not yet spoken publicly of his years held in Gaza.

He became a focus of intense popular attention in Israel, where tens of thousands of citizens pressured the government to make the deal it ultimately did. In a recent video appearance made for a celebration by the organizers of the campaign to free him, Mr. Shalit still appeared to be quite thin. He spoke shyly and breathed heavily as he expressed his gratitude to those who worked to free him.

Mr. Shalit decided not to make a personal appearance at the event, apparently because handling crowds after five years in a small, closed space remained difficult for him.

A magazine article a week ago in the mass-selling newspaper Yediot Aharonot, based on interviews with his friends, said Mr. Shalit had been riding his bicycle, playing table tennis in his backyard and displaying a healthy appetite for his mother’s cooking.

Mr. Shalit has had corrective surgery on his hand and elbow, where seven pieces of shrapnel had been lodged since his abduction.

Khaled Abu Aker contributed reporting from Ramallah, and Fares Akram from Gaza.

This article has been revised to reflect the following correction:

Correction: December 19, 2011
An earlier version of this article incorrectly stated that Izzedine Abu Sneineh had been convicted of throwing stones and hanging Palestinian flags from telephone poles.