According to Palestinian news agency Ma'an, the man was believed to be Samir Abd al-Rahman Yasin, a member of the Palestinian security forces.
A special unit of the Israeli military was taking part in an operation to capture an unnamed terrorist cell.
Qalqilya lies close to the 1967 green line with Israel and is just thirty minutes by car from the nearby Israeli city of Kfar Saba.
The incident came within twenty four hours of a separate operation by Israeli police forces in the Palestinian city of Jenin to arrest militants belonging to the Islamic Jihad terror group.
Israel radio reported that a member of Hamas was shot and killed in the subsequent exchange of fire.
No casualties or injuries were sustained by Israeli security personnel in either incident.
IDF spokesperson Lieutent Colonel Peter Lerner said the operation in Qalqilya "exemplifies the advanced intelligence and operational capabilities of the IDF" .
"The outcome of this mission makes Israeli life safer," he added.
