Police nabbed the duo at an upscale district of Manila following a tip-off from the Kuwaiti authorities late last month.
Police nabbed Husayn Al-Dhafiri and Rahaf Zina at an upscale district of Manila following a tip-off from the Kuwaiti authorities late last month, but the arrests were kept secret while Filipino authorities investigated further, officials said.
The pair had entered the country repeatedly in recent months as part of plans for "a bombing operation" either in the Philippines or Kuwait, Justice Secretary Vitaliano Aguirre told reporters.
Aguirre said Al-Dhafiri was an active IS member in the Middle East and said the United States authorities believed he could "pose a threat to the national security of the Philippines".
"He is alleged to have been involved in explosives manufacturing and possibly operational planning against Kuwait," Aguirre added.
He said Zina and Al Dhafiri married after her husband, a high-ranking IS commander, was killed in Syria.
The Filipino official said Al-Dhafiri would be deported to Kuwait while Zina would be sent back to Qatar from where she entered the Philippines.
"Both of them will be properly received by the security forces of those countries," he added.
The Kuwaiti embassy in Manila could not be contacted for comment.
Philippine President Rodrigo Duterte has previously warned that IS members might make their way into the Southeast Asian nation by infiltrating its Muslim communities, concentrated in the south of the largely Catholic country.
The Philippines has been battling for years with Muslim extremist groups in the remote southern region, some of whom have since pledged allegiance to IS.
Aguirre said he could not confirm if the two suspects had any contact with local extremists.