National Thawheed Jammath, or NTJ, and Jamathei Millathu Ibraheem, or JMI, would be banned by presidential decree, allowing the government to confiscate any property belonging to the two organisations, his office announced.
It follows the death of 15 people, including six children, after a military raid on a suspected terrorist safe house descended into a gun battle in the eastern coastal town of Kalmunai, near Sammanthurai.
The raid on suspects linked to the Easter suicide bombings turned violent after three explosions hit the building. Officials believe the blasts were caused by militants blowing themselves up as the search was underway.
Police spokesman Ruwan Gunasekara said that a woman and girl who survived the explosions were critically injured and are being treated at a nearby hospital in Ampara District.
The wounded woman and child are the wife and daughter of suspected mastermind of the bombings, Mohamed Hashim Mohamed Zahran, his family said.
“Yes, the wife and daughter were injured in the attack,” said Mohamed Hashim Mathaniya, sister of Zahran.
Isis claimed that three of its members had clashed with Sri Lankan police for several hours before detonating their explosive vests on them in Kalmunai, the militant group’s news agency Amaq said.
The group said 17 policemen were killed or injured in the attack, but did not give evidence for its claim.
Sri Lanka’s military said security forces recovered explosives, detonators, “suicide kits”, military uniforms and Isis flags during Friday’s raids.
The Easter suicide bombings, claimed by the Isis group earlier this week, targeted churches and hotels and killed at least 250 people.
The government said nine homegrown, well-educated suicide bombers carried out the attacks, eight of whom had been identified and one of whom was a woman.
Additional reporting by agencies
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