In another sign of the unravelling security, gunmen disrupted a meeting of the mainstream Fatah movement in the nearby city of Nablus.
Prime minister Ahmed Qorei said it was vital the Palestinians unite to prevent the kind of chaos seen last month in the Gaza Strip from spreading to the West Bank.
"We, the Palestinian people, must stand united in condemning this chaos in the same manner that we deterred the chaos that took place in Gaza," he said in an interview published in Sunday's Al Quds daily.
"If this chaos reaches the West Bank, then we will be on the verge of an unprecedented and unacceptable disaster."
However in a fresh challenge to the Palestinian Authority, around 5,000 people took to the streets of Jenin, in the northern West Bank, in support of the Al-Aqsa Martyrs Brigades, whose followers torched the local offices of the security services and district governor at the weekend.
Dozens of fighters fired their guns in the air, pledging support for the powerful local leader of the Brigades, Zakaria Zubeidi.
"Anyone touches him (Zubeidi), we will kill him. Anyone who touches him is a collaborator," the crowd chanted in unison.
Zubeidi had justified Saturday's arson attack on the security services by charging its officers were "co-operating" with Israel's Shin Beth domestic intelligence service to wipe out members of his organisation.
Al-Aqsa militants also ransacked the offices of the Jenin governor, Qaddura Musa, and tore down portraits of Palestinian leader Yasser Arafat from the walls to throw them in the fire.
Al-Aqsa has traditionally been loyal to Arafat but has become increasingly frustrated at what it sees as widespread corruption within both the Palestinian Authority and Arafat's mainstream Fatah movement.
Zubeida himself told Sunday's protest that he remained loyal to Arafat and criticised what he called unnamed "conspirators" who were trying to undermine the Palestinian leader, especially in the Gaza Strip.
"There are some Palestinian leaders conspiring against President Arafat," said Zubeidi, holding a portrait of the veteran leader.
"We declare that Al-Aqsa is against them and we fully support the president as we have (always) supported him," he said.
Further evidence of a breakdown in law and order came in the main northern city of Nablus on Sunday when gunmen from Al-Awda, another faction loyal to Arafat, fired into the air as a show of strength outside a Fatah meeting.
The 20 gunmen, who did not enter the building or injure anyone, prompted delegates to temporarily abandon the meeting before reconvening at a nearby refugee camp.
Three foreigners were also briefly held hostage on Friday night in Nablus.
Negotiations minister Saeb Erakat said the "chaos" was undermining the Palestinian cause. "We need to maintain and protect our national unity and we need to work out solutions to all problems through national dialogue involving everybody under the rule of law," he told AFP.
The latest bout of kidnappings and protests follows similar unrest in Gaza last month that prompted Qorei to submit his resignation before later agreeing to stay in his post. Mohammed Dahlan, former premier Mahmud Abbas' security minister and who remains a dominant figure in Gaza, warned of more mass protests in the territory if reforms are not implemented within days.
"The situation in Palestine can no longer tolerate corruption, and reforms decreed by Arafat should be implemented," Dahlan, who has denied being behind last month's unrest in Gaza, told the Kuwaiti newspaper Al-Watan.
If these reforms are not implemented by August 10, "huge protests numbering 30,000 Palestinians will take to the streets of the Gaza Strip," said Dahlan, who accused Arafat of "sitting on the corpses and destruction of Palestinians at a time when they are in huge need of support and a new mentality".
The Israeli military, meanwhile, said two people were slightly wounded Sunday when a home-made rocket fired by Palestinians from the Gaza Strip landed in southern Israel.
Israeli forces have been operating for more than a month in the town of Beit Hanun in northern Gaza in a bid to put a halt to the firing of the Qassam rockets, named after the armed wing of the radical Islamist movement Hamas.