The incident occurred in the northern Sheikh Radwan neighbourhood with the interior ministry identifying the gunman as 27-year-old Yussef al-Hatar, a local leader of a group of Islamic extremists known as Salafists.
According to ministry spokesman Iyad Buzum, the security forces had gone to his home in the morning to arrest him for unspecified "illegal activities."
But Hatar tried to flee, firing on the forces as he went. He tried to blow himself up with a suicide vest but was shot dead before it detonated, Buzum told AFP.
"Security forces barricaded the house and then intense clashes erupted," witnesses told AFP, some of whom identified Hatar as being a member of a group affiliated with the Islamic State jihadist group.
Inside the building, security forces found a number of weapons including "explosive belts, explosive devices and rocket-propelled grenades," Buzum said.
Pictures of the weapons were posted on the ministry's Facebook page.
Hamas, the de facto power in Gaza, has in recent months been waging a harsh crackdown on Salafist groups operating in the enclave following a series of unclaimed bomb attacks.
They have hit public buildings and private homes and cars, but have also targeted officials of both Hamas and the rival Fatah movement headed by Palestinian president Mahmud Abbas.
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