A woman claiming to be the wife of an Australian Islamist preacher arrested in the Philippines says he was not involved in any terrorist activity.

Musa Cerantonio, 29, who has been described as "an inspiration" to jihadists worldwide, has emerged as one of the most popular and influential online preachers supporting the jihad in Iraq and Syria.

Cerantonio was arrested on Friday in the central Philippines city of Lapu-Lapu before being taken to Manila, where he is awaiting deportation.

Joan Montayre, 32, was also arrested and is now in jail facing unrelated charges of swindling.

Ms Montayre says she married Cerantonio last year and was living with him in the central Philippines before the arrests.

She told authorities Mr Cerantonio was a good person, but confirmed he had been uploading videos to the internet to spread Islamic teachings.

Mr Cerantonio is being detained in a large police camp in Manila.

It is expected that he will be deported to Australia if he is cleared of any charges.

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

They say there is no evidence linking the preacher to any act of terrorism.

Philippines police say Mr Cerantonio was arrested at the request of the Federal Government and that he is expected to be deported.

However, whether Mr Cerantonio has broken any Australian laws remains unclear.

Preacher called on followers to support Islamic State

Earlier this month, Mr Cerantonio announced on Twitter that he was headed to Syria. Last week he said he had arrived.

He 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.

Mr Cerantonio's arrest comes after the Australian Government outlawed the Islamic State, and listed it as a terrorist organisation. The move replaces the former listing of the Islamic State of Iraq and Syria, also known as ISIS.

Foreign Minister Julie Bishop has said the arrest is concerning.

"But it's obviously before the authorities at present, so I don't want to say anything to jeopardise to work of the Philippines security agencies and police authorities," she said.

Last month, Prime Minister Tony Abbott said the Government would do whatever it could to protect Australian citizens from extremists returning to the country.

"We will ensure we stop the jihadists as well, because the last thing we want is people who have been radicalised and militarised by experience with these Al Qaeda offshoots in the Middle East returning to create mischief here in Australia," Mr Abbott said.