A police spokesman said that three suspected suicide bombers were among the 15 dead after the shoot out.
The gunbattle began this morning after police tipped off soldiers to a suspected safe house, where authorities say the militants set off three explosions and opened fire.
The additional violence comes after a group of attackers targeted six hotels and churches and killed roughly 250 people, many of whom were Christians celebrating Easter.
The Islamic State has claimed the three militants who blew themselves up during a fierce gun battle with security forces in Sri Lanka's Eastern province, a media report said on Sunday.
The archbishop said earlier this week that he had seen an internal security document warning of further attacks on churches and said there would be no Catholic masses celebrated anywhere on the island on Sunday.
The clashes came hours after security forces raided a nearby location where they believe Hashim and other suicide bombers recorded a pledge of allegiance to ISIL leader Abu Bakr al-Baghdadi before carrying out the bombings of three churches and three hotels.
Following the deadly blasts, the Islamic State claimed responsibility for the attacks and subsequently released an image of eight suspected bombers.
Of the 15 people found dead in the house following the raid, six are suspected terrorists and nine are civilians, including six children, Maj.
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During the sweeping raids, military officials said security forces discovered explosives, detonators, "suicide kits", military uniforms and Islamic State group flags. "'We don't want repetitions, ' Ranjith said".
"That is why the kind of detailing of the incident they received was very, very specific", Mr Sahni said.
Sirisena tried to sack Wickremesinghe past year, and experts believe the feud could have played a part in Sri Lanka's failure to act on intelligence warnings given weeks before the attacks.
It was an extraordinary request for a Catholic clergyman to make, as churches often remain a refuge.
"If we had any inkling, and we had not taken action, I would have handed in my resignation immediately", he said, adding: "But what do you do when you are out of the loop?"
A grieving woman is supported during a funeral service for Easter Sunday bomb blast victims at St Sebastian Church in Negombo, Sri Lanka.
"Every household in the country will be checked", President Maithripala Sirisena told a news conference, according to a statement.