Aljazeera's Palestine bureau chief Walid al-Umari said on Tuesday that Palestinian prisoners were injured when a large Israeli force stormed Ofer military detention centre, west of Ram Allah.
Isa Qaraqaeh, the head of the Palestinian Prisoners Association, said the troops entered as four members of the Popular Front for the Liberation of Palestine (PFLP) were due to be transferred to another prison.
When prisoners tried to prevent the transfer of their fellow inmates, soldiers opened fire with teargas and rubber-coated metal bullets - which can be deadly.
Prisoners hurled objects at Israeli guards and allegedly set fire to six tents.
A total of 20 prisoners were wounded, at least one seriously, added Qaraqaeh.
Among the wounded was deputy secretary-general of the PFLP Abd al-Rahim Malouh, whose lower jaw was fractured.
Malouh was among the prisoners being moved. He is serving a seven-year term after being convicted by an Israeli military court last year for membership of what Israel calls a terrorist organisation.
An Israeli military spokeswoman said 40 guards were "very lightly injured", mainly by inhaling gas.
Calm was eventually restored at around dawn and the four prisoners were transferred.
The Palestinian resistance group Hamas condemned the clashes and said the Israeli authorities should be held accountable for any wounds suffered by prisoners.
Around 1100 Palestinians are held at the detention centre, which is on the Ofer military base.