In Ramallah, 50 fighters loyal to Fatah and 200 activists stormed a Palestinian parliament building, dragging a Hamas-backed deputy speaker from the building.
In Hebron, al Aqsa Martyrs Brigades fighters, an offshoot of Fatah, stormed government offices and set up checkpoints to search for Hamas members.
Fatah members also destroyed an Islamic school's offices and local television and radio in Nablus in apparent revenge attacks.
Hamas later threatened to retaliate in the West Bank against Fatah - which is headed by Mahmoud Abbas, the Palestinian president - if it did not stop "terrorism" there.
Sami Abu Zuhri, a Hamas official, said 150 Hamas supporters had been "abducted" in West Bank.
"What is happening in the West Bank is a real coup and real terrorism," he said.
"We will not stand handcuffed against these crimes in the West Bank.
In Gaza, looting of Fatah buildings also continued including from Abbas's bullet-scarred seafront presidential compound and the home of former president and Fatah leader Yasser Arafat.
Many Fatah supporters who live in Gaza fear reprisals from Hamas fighters.
Hamas fighters are still searching for their Fatah rivals to seize their weapons and at least 200 Fatah men have already fled the territory, by land or sea to neighbouring Egypt.
Israeli troops at the Erez checkpoint between Gaza and Israel fired warning shots at Palestinians who tried to cross into Israel to escape the violence.
Hanan Ashrawi, a Palestinian Legislative Council member, told Al Jazeera that "Palestinian leaders, including from Al Aqsa Martyrs Brigades, have called on people not carry out acts of revenge in the West Bank".
Ashrawi, however said the looting of buildings such as Yasser Arafat's were "acts of extreme provocation".
Abbas is expected to swear in a new prime minister and emergency cabinet within the next 24 hours.
Abbas asked Salam Fayyad, the independent finance minister in the now disbanded unity government, to form a new cabinet after Hamas fighters took full control Gaza Strip.
In a boost for Abbas, the US will lift a direct ban on aid to the government once the new administration is announced, a US envoy told Abbas during a meeting in the West Bank.
The emergency government will have between 10 and 12 members and consist primarily of independent technocrats, he said.
"Most crucial will be the position of the minister of interior who will be in charge of security in the West Bank, and the Gaza Strip if possible," Walid Batrawi, Al Jazeera's correspondent in Ramallah, said.
"We might see some Fatah officials but, of course, none of the Hamas people because the Palestinian Authority and the president consider that Hamas has carried out a coup."
Separation ruled out
Ismail Haniya, the former prime minister who has refused to accept his firing, has ruled out setting up a separate state ruled by Hamas in the Gaza Strip.
"Gaza belongs to all the Palestinian people and not just Hamas," he said in an interview with France's Le Figaro newspaper.
"Separation is not on the agenda and never will be."
Late on Friday, Khaled Meshaal, the exiled political leader of Hamas, called for dialogue with Abbas and Fatah.
At a news conference in the Syrian capital Damascus, he said Hamas had no option but to use force to wrest control of Gaza in fighting that killed dozens of Palestinians.
"What is needed now is to deal with the Palestinian schism. Hamas is for Arab sponsorship of a dialogue in the Palestinian national interest.
"The lack of security drove the crisis toward explosion. What happened in Gaza was a necessary step. The people were suffering from chaos and lack of security and this treatment was needed."
Meshaal called for the Palestinian security forces to be reorganised and said elements in Fatah that he did not want to identify were to blame for the lack of security in Gaza.
"We need to restructure the Palestinian security apparatus to be a national force chosen according to merit and not on a factional basis," he said.