One prisoner from the West Bank who was on the release roster for Monday was found to have changed allegiance in jail, from Fatah to the Hamas movement, and was held back, the Israel Prisons Service said.
Road to freedom
Two buses left the Kitsyot prison in southern Israel carrying the 57 detainees around 11:30am (0930 GMT) and headed to the Beitunya checkpoint.
9,850 Palestinians remain in Israeli jails.
105 are women.
359 are children.
40 Palestinian Legislative Council members are also under arrest.
Marwan Barghouti, a member of Fatah's Revolutionary Council, is one of the most prominent detainees and is seen as a potential future Palestinian leader.
Sources: Palestinian Ministry for Prisoner Affairs (July 2006), B'Tselem (Oct 2006)
A third bus, which was supposed to leave for the Erez crossing into the Gaza Strip with the other 29 men, remained at the prison.
The office of Ehud Olmert, the Israeli prime minister, said the men from Gaza would be released on Tuesday, one day later than planned.
A statement said Shimon Peres, the Israeli president, signed all of the Gaza pardons after an unexplained delay.
A spokesman for the Israel Prisons Service blamed the delay on "technical problems" that did not originate with the agency.
Peres's signature was not required for the release of West Bank-based prisoners because the area is under military occupation and the men were freed in accordance with an order signed by an Israeli general
The Israeli cabinet approved the release of 87 Palestinian men, including two minors, a week ago.
The majority of the men on the release roster were members of Abbas's Fatah faction, with the rest coming from the smaller Popular Front for the Liberation of Palestine (PFLP) and the Democratic Front for the Liberation of Palestine (DFLP) groups.
The freeing of prisoners is emotionally charged for Palestinians, who see their nearly 11,000 brethren held in Israeli jails as fighters for freedom from Israeli occupation.
Before the prisoners arrived, groups of Palestinians had already assembled at the Erez terminal.
"There is a mood of celebration here in Gaza," Nour Odeh, Al Jazeera's correspondent at the crossing, said.
"Although the number of prisoners is not very large, it's always a cause for celebration."
But many Israelis say such amnesties encourage violence by Palestinian fighters.
Olmert said only prisoners "without blood on their hands" and willing to sign a document renouncing violence would be freed.
Olmert and Abbas are to meet on Wednesday to discuss their agendas for a US-sponsored conference on Palestinian statehood.
The talks will host Olmert and Abbas alongside other Arab leaders, but exclude Hamas.
Palestinians are divided on whether the conference will do anything to bring them closer to statehood.