An Australian teenager jailed in Lebanon on accusations he was trying to join Islamic State (IS) has allegedly confessed he was encouraged to become a foreign fighter by the head of a Sydney-based charity which has been under a cloud of suspicion by Lebanese and Australian authorities.

The explosive allegation is contained in a Lebanese court dossier, obtained by the ABC, in the military tribunal case of 19-year-old Isaak el Matari, from Sydney, who has spent the past nine months in Lebanon's notorious Roumieh jail accused of planning to travel to Syria to join IS.

Warning: Contains an image that may distress some readers.

Matari interrogated by Lebanese intelligence

Mr Matari was arrested by Lebanese security forces in the northern city of Tripoli on August 31 last year, less than two weeks after he secretly flew to Lebanon, shocking his Sydney family.

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In a statement announcing his arrest last year, the Internal Security Forces said the teenager, who it identified only as "AM", was two days away from travelling across the border to Syria and had been monitored communicating with IS terrorists, including a foreign IS "coordinator", about his plans to join the group.

Over the past nine months, Mr Matari has been brought before Lebanon's military tribunal and been interrogated by the country's intelligence agencies, which say he has provided information about Australian IS fighters, supporters and funders.

Isaak el Matari posted this photo of himself next to a slaughtered sheep a few days after he arrived in Lebanon. ( Facebook )

Matari released and ready for deportation

The ABC understands Lebanese authorities are now preparing to deport the teenager to Australia, where he is expected to come to the attention of Australian counter-terrorism authorities.

Security sources have told the ABC Mr Matari was released from Roumieh prison on Friday into the hands of Lebanon's General Security intelligence agency for final interrogations in the capital Beirut before his imminent deportation to Australia.

The Australian Federal Police have refused to confirm whether they are investigating Mr Matari or planning to lay charges against him upon his return.

Charity boss urged him to join IS, says teen

The ABC has obtained a summary of Mr Matari's interrogations prepared for the military judge who heard his case, saying the teenager had confessed he wanted to join IS because he was "shocked by the bloody repression in Syria".

A 2015 post from the Arabic Facebook page of Dar al Quran wa Sunnah, showing Osama bin Laden.

The court dossier said Mr Matari had told interrogators he had been encouraged to join IS in Syria by Sydney man Adnan Baradaaji, who is the head of Australian charity Dar Al Quran Wa Sunnah.

The charity, which is based in Sydney and Tripoli, was established to raise money for Syrian refugees but Lebanese authorities accused several of its members of fundraising and recruiting for IS.

Lebanon's military prosecutor issued an arrest warrant for Mr Baradaaji in 2015 in absentia on allegations of fundraising for jihadists.

Ibrahim Barakat in a still from a video thanking Australians for donations. ( ABC )

Several other members of the charity have been charged in Lebanon including the founder of its Lebanese arm, Ibrahim Barakat, who was arrested in 2015 and described himself to Lebanese interrogators as the religious leader of IS in the country's north.

Lebanese prosecutors have accused Mr Barakat of fundraising and recruiting for IS, and of leading clashes by militants against the Lebanese Army in Tripoli in 2014.

Sources close to Mr Matari have told the ABC he was involved with the charity before he left for Lebanon.

According to Mr Matari's court dossier, he told interrogators he had planned to sneak into Syria through the Lebanese border town of Arsal, which is the site of a sprawling refugee camp where Dar Al Quran Wa Sunnah claims to operate.

The charity's president, Adnan Baradaaji, in the Lebanese city of Tripoli in a photo posted on Facebook in 2014. ( Facebook )

The charity has released several videos of its members handing out aid in the camp.

Mr Matari allegedly told interrogators that after clashes broke out in Arsal between jihadists and the Lebanese Army last July, he decided to take another route to Syria from Lebanon's far north.

The accuracy of Mr Matari's alleged statements have not been tested in the military tribunal proceedings, where Mr Baradaaji has not been represented by a lawyer.

Human rights groups have previously accused Lebanese authorities of torturing suspects and forcing them to provide false evidence.

Sydney charity targeted by Australian police

Dar Al Quran Wa Sunnah has also been the target of counter-terrorism police investigations in Australia.

In 2016, two of its members' homes were raided in an Australian Federal Police operation targeting a multi-million-dollar fraud on Australia's family daycare system which police suspected was funding IS.

Senior counter-terrorism sources have told the ABC the operation was investigating intelligence that more than $13 million in Commonwealth childcare benefits and subsidies was funnelled to the terrorist group.

The charity's then secretary, Ali Assaad, was arrested and pleaded guilty to a fraud offence totalling only $5,080.

Mr Assaad was handed a good behaviour bond for dishonestly intending to cause a loss and knowingly making a false or misleading statement.

No conviction was recorded and he was ordered to repay the Commonwealth.

Organisation still registered as a charity

Dar Al Quran Wa Sunnah continues to operate as a charity in Australia, registered by the Australian Charities and Not-for-profits Commission (ACNC).

Isaak el Matari uploaded this photo of himself as a younger man. ( Facebook )

The charity collected nearly $1.9 million in donations from Australians in the past two years, according to financial statements lodged with the ACNC.

The ACNC yesterday refused to answer whether it had taken any action against Dar Al Quran Wa Sunnah, despite telling the ABC in 2015 that the charges against Mr Barakat in Lebanon would "absolutely" trigger an investigation.

"The ACNC has both information and monitoring powers to help us investigate concerns regarding the activities and operations of registered charities," a spokesman said in a statement prepared for the ABC.

"Where we find evidence of misconduct or mismanagement, we take action."

A spokesperson for Australia's Department of Foreign Affairs and Trade confirmed it was providing consular assistance to "an Australian man detained in Lebanon" but declined to provide further comment "owing to our privacy obligations".

The ABC has contacted Mr Baradaaji and Dar Al Quran Wa Sunnah for comment.