The minister, Shaul Mofaz, spoke a day after an Israeli air strike against an ice cream truck killed two Islamic Jihad militants and three bystanders - one child and two teenagers - in Gaza City.
Hamas swept January parliamentary elections and is forming a Cabinet.
It has rejected international calls to renounce violence and recognise the state of Israel but has maintained a year-old moratorium on suicide bombings.
Mofaz told Israel's Army Radio that Israel's policy of assassinations had proven to be effective and would continue.
"There is no question about its efficacy," Mofaz said. "Look what happened to Hamas in the years it conducted a suicide bombing war against us. When we started the targeted killings, the situation changed," he said.
"We will continue the targeted killings at this pace," Mofaz added. "No one will be immune."
Asked if Haniya would be a target if Hamas were to resume attacks, Mofaz replied: "If Hamas, a terror organisation that doesn't recognise agreements with us and isn't willing to renounce violence, presents us with the challenge of having to confront a terror organisation, then no one there will be immune. Not just Ismail Haniya. No one will be immune."
Salah al-Bardawil, a Hamas spokesman, denounced Mofaz's comments.
"This statement and Israeli practices on the ground reflect the bloody, inhumane and inflammatory character of the Zionist enemy," al-Bardawil said. "We are not seeking immunity or mercy from Israel. We are in a confrontation. The side that is most steadfast is the side that will survive."
Hamas headed into a domestic confrontation on Monday by stripping the president, Mahmoud Abbas, of powers his Fatah Party granted him in its last session.
Fatah delegates walked out of parliament in protest, saying that Hamas was twisting the rules to nullify Abbas' additional authority. A Fatah official said they planned to extend their protest by boycotting the parliamentary session on Tuesday.
The Hamas-Fatah conflict has been simmering since Hamas swept Fatah out of office in January, winning 74 seats in the new parliament to Fatah's 45.