Ermita announced the arrest of Taufiq Rifqi, two weeks after he was captured by military intelligence agents in Cotabato City.
Rifqi is next in rank to Hambali, the suspected JI operations chief who was recently arrested by operatives of the US Central Intelligence Agency (CIA) and the Thai police.
Ermita revealed the arrest in an earlier interview on ABS-CBN but did not identify the suspect by his full name or nationality.
"If I recall right, about a week ago, the number-two leader by the name of Taufiq, alias Abu Obaidah, was also arrested in Cotabato," Ermita said.
The military had previously refused to confirm that they had made an important JI arrest in Cotabato.
Armed Forces vice chief Lt. Gen. Rodolfo Garcia said earlier this month that "an arrest has been made" in Cotabato, but would not reveal the identity of the suspect or confirm whether the detainee is a JI operative.
Both Rifqi and Hambali are wanted by Singaporean authorities for planning to bomb the US and Israeli embassies in the city state.
They managed to slip through a police dragnet even after several suspected JI operatives were arrested.
Authorities have also averted a supposed JI plan to carry out bomb attacks region wide, including the Philippines.
With Rifqi’s capture, it also indicated the JI is using central Mindanao as launching point to carry out terror attacks in Southeast Asia.
Sources in the military also disclosed Rifqi is overseeing the training of recruits somewhere in the jungles of central Mindanao.
Armed Forces spokesman Lt. Col. Daniel Lucero said the military will be formally presenting Rifqi before the media "in a matter of days."
But Lucero clarified they are gathering evidence on Rifqi’s supposed links with the JI and his possible involvement in terror activities in the country. -With AFP, AP