The army said two other Palestinians, who were injured in the shooting, had been taken to an Israeli hospital and questioned.
The army said all three men were responsible for recruiting suicide bombers and planning attacks against Israelis.
Palestinian officials said that Mohammed Hamad, an al-Aqsa commander, was shot down by undercover Israeli troops during the attack in Tulkarem.
The group said another man was arrested in the raid.
Mahmoud Abbas, the Palestinian president, and Ehud Olmert, the Israeli prime minister, announced a tentative ceasefire in the Gaza Strip on November 26, but it has not been extended to the West Bank where Israeli military operations continue.
The truce was seen as prelude to a renewed peace effort by the two sides.
On Tuesday, Olmert visited Jordan to discuss the stalled peace talks, Jordanian palace officials said.
"Agreement was reached on continuing co-ordination with the Palestinian Authority to discuss all the avenues that will allow reactivating the peace process," the palace source said.
Olmert's office said earlier he and King Abdullah talked about the Palestinian power struggle and other regional issues.