Authorities in the Philippines will deport a high-profile Australian preacher who has voiced support for Islamist militants fighting in Iraq and Syria.

Philippines-based Musa Cerantonio, 29, was arrested in the central Philippines city of Lapu-Lapu and taken to Manilla where he is awaiting deportation.

Mr Cerantonio, born in Melbourne to an Italian family, converted to Islam at the age of 17 and is now one of the most popular online preachers supporting the militant group previously known as Islamic State of Iraq and Syria (ISIS).

Authorities in the Philippines say they want to know if Mr Cerantonio has recruited Filipino Muslims on social media sites to support rebels in Iraq and Syria.

Philippines regional police head Prudencio Banas says a warrant for deportation has been served to Mr Cerantonio by immigration officials, who had him under surveillance for a week.

Regional deputy police chief superintendent Conrad Capa said Mr Cerantonio was arrested at a one-room apartment which he is believed to have shared with a Philippine woman.

"He has been in [the region of] Cebu since February... for the most part, he keeps to himself in his rooms, in hotels or apartments," Mr Capa said.

"We cannot say with certainty that he had any contact with local Muslim groups."

The 32-year-old woman was wanted by police over an unrelated fraud case and was also arrested Friday, he added.

He said the pair had been periodically moving around Cebu, and that the woman had been buying food and other supplies for Mr Cerantonio.

A Philippine police intelligence officer involved in the operation said Mr Cerantonio had been in Mindanao, though there was no indication he had tried to recruit people or been in contact with Islamist militants in the area.

"This person... has a website and he propagates extreme teachings and advocates jihad and calling on Muslim brothers to go to Syria and Iraq to fight together with the ISIS," said the official, who asked not to be named.

Cerantonio had pledged to join fighters in Syria

Foreign Affairs Minister Julie Bishop last month said she had cancelled several passports of Australians known to be fighting with extremists, on advice from intelligence agencies.

Earlier this month the preacher announced on Twitter that he was headed to Syria, and last week he said he had arrived.

Melbourne-born Muslim preacher Musa Cerantonio has spoken publicly of his support for Islamic State. ( Youtube )

Mr Cerantonio has also tweeted support for Abu Bakr Al-Baghdadi, the head of the Islamic State, who has proclaimed an Islamic caliphate encompassing areas of Iraq and Syria.

"Sometimes he mentions the Philippine government [on his website], but does not call for violence," the intelligence officer said, adding that Mr Cerantonio has "no overt following" in the Philippines.

Television footage aired by the ABS-CBN network showed a bearded Caucasian man in a white robe being ushered out of an apartment by officers wearing helmets and flak jackets.

A media officer at the Australian embassy declined to comment when asked about the arrest.

The AFP says as it is an ongoing matter for Philippine authorities, it would not be appropriate to comment further.

The Philippines has a large Muslim minority in the southern region of Mindanao, a hotbed for a decades-old Muslim insurgency and where Islamic militants linked to Al Qaeda also operate.

ABC/AFP