Hamas took total control of the Gaza Strip two weeks ago when members of its armed wing forced the Fatah-dominated security forces out of the coastal territory during several days of violent clashes.
"The refusal by the US, EU et al to deal with Hamas reflects their disrespect for the wishes of the Palestinian people"
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Abbas responded by dismissing the Hamas-led unity government and swearing in a new emergency cabinet which only has effective control in the West Bank.
Previous attempts to disarm armed men from Hamas, the pro-Fatah al-Aqsa Martyrs' Brigades and other smaller groups in the West Bank have failed.
Ahead of the announcement, a senior commander of the al-Aqsa Martyrs Brigades told Al Jazeera that he did not believe that Abbas would attempt to take their weapons off them.
"I think Abu Mazen [Abbas] mentioned the illegal militant groups, I don't think he means us. He means illegal weapons that we used against the Palestinians," Zakaria Zubeidi, the group's commander in the West Bank, said.
"Formally we are illegal, but on the real ground we are official and we are legal because there are occupiers. As soon as we get back our land we don't need to hold these weapons."
Meanwhile, Abbas on Wednesday dismissed several more security chiefs over the defeat in Gaza. Those dismissed included General Misbah al-Bheisi, head of his presidential guard, Colonel Ziyad Judeh, his deputy, and Colonel Manar Mohammed, the commander of an elite security unit, an official said on condition of anonymity.