Hussein al-Dhafiri was arrested in an upscale district of Manila late last month along with his Syrian wife Rahaf Zina on suspicion of being members of IS and of planning attacks in both countries.
He was deported to Kuwait on Friday to stand trial in his home country on charges of membership of a banned organisation and of plotting attacks.
His wife, whom he married after her high-ranking IS commander husband was killed in Syria, remains in custody in the Philippines pending deportation to Qatar, from where she entered the islands.
They face similar charges to Dhafiri, the paper added.
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Philippine Justice Secretary Vitaliano Aguirre said on Thursday that Dhafiri was suspected of manufacturing explosives and of possible operational planning against Kuwait.
Washington believed he could "pose a threat to the national security of the Philippines," Aguirre added.
A statement issued by the Kuwaiti embassy in Manila on Friday said evidence was obtained by the emirate's security services that Dhafiri was "planning to carry out terroristic attacks in the State of Kuwait."
In June 2015, a Saudi blew himself up in a Shiite mosque in Kuwait City, killing 26 worshippers in an attack claimed by the Sunni extremists that was the deadliest in the emirate's history.