A crowd of about 200 rioters confronted the soldiers shortly after they arrived in the town of Qalqiliya and surrounded a home where a wanted Hamas fighter was believed to inside.
Palestinian witnesses said larger numbers of troops were moving into Qalqiliya as the operation continued.
In another incursion, an Israeli Apache helicopter fired two missiles into the home of a local leader of the Ezzedine al-Qissam Brigades, witnesses said.
There were no casualties reported in the strike which singled out the home of Alaa Aqilan, a local commander of a Hamas-controlled police force in the Shatti Refugee camp in Gaza City.
Minutes later, a second strike hit a home in the Zeitoun neighbourhood on Gaza City's eastern fringe.