A video journalist with the agency, Italian Andrea Bernardi, was thrown to the ground and jabbed in the side with a weapon.
He was held on the ground by a soldier, one knee compressing his chest, until he managed to show his press card.
Bernardi suffered bruised ribs and an injury under the eye.
Israeli soldiers pointed their weapons at him and his colleague, Palestinian photographer Abbas Momani.
They smashed a video camera and a stills camera and took away another camera and a mobile phone.
At the time both journalists were wearing body armour clearly marked "Press".
The incident was filmed and posted online by a local production company.
The pair had been covering clashes between Palestinians and soldiers when some troops took them aside, swore at them in English and told them to stop recording events.
AFP has protested to the Israeli military over the incident and said it intends to file an official complaint.
"Disciplinary measures will be taken," army spokesman Colonel Peter Lerner told the agency.
"The highest levels of command are aware of the incident," he said, specifying that this includes the head of Israeli forces in the West Bank.
In an incident on April 24, the Palestinian AFP photographer manhandled Friday and a Palestinian colleague had stones thrown at them by Israeli soldiers.
That incident was also filmed, and the army announced that disciplinary action would be taken against the soldiers involved.
Friday's clashes between Palestinians and troops at Beit Furik came after the funeral of Ahmed Khatatbeh, 26.
He died of his wounds after being shot by soldiers near Nablus in the northern West Bank. The army said he and another man had thrown a petrol bomb at a vehicle on a road to the Jewish settlement of Itamar.