Medical sources said that 11 people were wounded during the raid, including members of the security forces and civilians who were residents of the building where the militants were hiding.
Security forces pulled the bodies of three suspected militants from the wreckage of a building in a central Jordanian city on Sunday following a shoot-out in which at least four security personnel were also killed, the government said.
There was no immediate claim of responsibility for Friday's bomb blast in Al-Fuhais, a mostly Christian town, and the identities of the suspects were not known.
Jordan is a close Western ally in a turbulent region, and has largely been spared from the conflicts in neighboring Syria and Iraq.
The shoot-out in the city of Salt, northwest of the Jordanian capital, Amman, came after a home-made bomb exploded on Friday under a patrol auto at a music festival, killing one security force member and wounding six.
Ambulances, bulldozers and police cars were deployed around the building in the Naqab al-Dabour residential neighbourhood in Salt, television footage showed.
Witnesses heard several strong explosions near the site which a security source said were explosives being detonated by the police as they closed in on the militants.
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Ghuneimat initially said one officer was killed, but later updated the death toll to three.
The clash that began late on Saturday was among the deadliest between insurgents and Jordanian security forces in recent years. The attack on Saturday killed a security man and injured six others, Saudi Press Agency said.
"The building in which the terrorist cell was found is about to fall and will be demolished to prevent a sudden collapse", Ghunaimat added.
Ghneimat said that the security forces raided the house in Salt after receiving a tip-off. Prime Minister Omar Razzaz called Friday's bombing a "terrorist attack".
The United States "strongly condemned" the attacks against Jordanian security forces in Al-Fuhais and in Salt, in a statement released Sunday by its Amman embassy.
Security forces have been extra vigilant with warnings that sympathisers of Islamic State could launch revenge attacks after the militants were driven out of most of the territory they once controlled in Syria and Iraq.