Mahmoud Afif Abdeljalil, 51, was detained on July 4 on Mindanao island, southern Philippines, and will be deported for illegal entry.
The Jordanian, who assumed a fictitious identity and used fake documents to reside in the country, was a "henchman" of Bin Laden's brother-in-law Mohammed Jamal Khalifa - a Saudi businessman also linked to Al Qaeda who was killed in Madagascar in 2007, the immigration bureau said in a statement.
"We are going to deport him (Abdeljalil) for being an illegal entrant as he has no record of arrival, after he was arrested and deported in 2003 for being an undesirable alien," Bureau of Immigration Commissioner Jaime Morente was quoted as saying by Efe news.
Authorities have been monitoring Abdeljalil's activities since August 2018, when he and an Algerian man were flagged down at a military checkpoint in Mindanao's Zamboanga city.
He was detained in the same city in July following a joint operation between immigration, military and police of Zamboanga.
During interrogation, Abdeljalil said he had returned to the Philippines in 2007 after being deported in 2003 due to the expiration of his visa and "involvement in clandestine terrorist activities as a Palestinian under the name Mahmood Afif," the statement said.
Upon his arrest 16 years ago, authorities established that Abdeljalil was "the point man" in the Philippines for Bin Laden's brother-in-law Khalifa in managing charity organizations that transferred money to Al Qaeda and local terrorist group Abu Sayyaf, which is currently linked to the Islamic State, it added.
That time, the Philippines' central bank also froze Khalifa's accounts and financial assets to stop the funds being transferred to terror groups.
Even after Khalifa's death in 2007, Abdeljalil continued to financially support Abu Sayyaf through several mosques and madrasas he built in the south, which received foreign funding from Al Qaeda, the statement said.
Abdeljalil's arrest comes at a time when Philippines authorities are extremely vigilant in Muslim Mindanao, which is suspected of becoming a haven for more radicalized foreign terrorists who have fled the Middle East after the fall of the Islamic State caliphate.
( With inputs from IANS )