The unit, which Fatah officials said has about 2,500 members, is in response to a new Hamas militia that the government deployed last month, over the objections of the president, Mahmoud Abbas, who also is the leader of Fatah.
The presence of a new Fatah militia, in addition to the official security branches that the movement dominates, could worsen tensions between Fatah and Hamas that have already erupted in deadly violence and led to fears of a civil war.
The new unit gathered in Jenin on Saturday morning, wearing black T-shirts emblazoned with "special protection unit" on the back and a photo of Yasser Arafat, the late Palestinian leader, on the front.
A few dozen were armed with assault rifles while several others carried pistols.
"You are here to protect your people and the Palestinian Authority institutions," Ata Abu Rmeileh, a Fatah leader in Jenin, told the unit through a loudhailer.
Chanting Fatah's name, the force split into 23 groups and marched through the streets of Jenin.
The deployment of the militia on Saturday was intended to drive home the message that unless Hamas disbands its new force, then Fatah will create parallel units across the West Bank and Gaza Strip, Fatah officials said.
The officials added that Hamas may be organising its own militia in the West Bank but this could not be confirmed.
Hamas' deployment of a militia
in Gaza in May led to clashes
Control over security forces is a key element in the power struggle between Abbas, who hopes to restart peace talks with Israel, and Hamas, whose refusal to renounce violence or recognise the state of Israel has led to international sanctions.
Hamas launched its new militia in Gaza in May after Abbas took command of all of the powerful Palestinian security branches.
The deployment led to clashes on Gaza's streets with regular police and security forces loyal to Abbas, and several people were killed.