A spokesman for the Internal Security Ministry said the police would issue warnings on Wednesday to four Palestinian offices that must close within 48 hours.
Most of the Palestinian offices are shuttered, their leaders asked to remain silent or to move.
Bomb supplies and disguises for suicide bombers were found in the headquarters of the Palestinian office of preventive security, they said.
Most of the Palestinian Authority's offices responsible for Jerusalem affairs are located in the town.
Israel retaliated with missile strikes against Palestinian offices in Gaza City.
Other Palestinian offices in East Jerusalem, including a statistics bureau and a housing council, work in coordination with the authority.
Exercise of governmental activity, and location of Palestinian governmental offices, would be as specified in the Interim Agreement.
First, Israel seized Palestinian offices in Jerusalem, including the symbolically important Orient House.
The Palestinian Authority was served with an order to close four Palestinian offices in East Jerusalem.
Early Friday, its army and police force took over nine Palestinian offices in and around eastern Jerusalem.