Dozens of mosques across Indonesia are under surveillance for supporting the Islamic State (IS) terrorist group, spreading its ideology and recruiting fighters to go to Syria.

Key points: Researchers attended mosques and Koran reading groups for information

Researchers attended mosques and Koran reading groups for information IS sympathisers increasingly holding private meetings

IS sympathisers increasingly holding private meetings Mosque accused of preaching the IS ideology denies claims

The ABC can reveal 41 mosques across 16 Indonesian provinces have been implicated in research conducted on behalf of the Indonesian Government.

Of those, 16 mosques in seven provinces have been officially confirmed as supporting the IS group by a team of researchers who have, and continue to, secretly infiltrate the places of worship.

In an exclusive interview with the ABC, the head of the research team and Indonesian terrorism analyst Adhe Bhakti said Islamic boarding schools and Koran reading groups were also being used as places to preach the radical IS ideology.

"We found different forms, different functions of the mosques," Mr Bhakti said.

"Some were purely used as a place to spread ideology, some were used as a place of consolidation, even the caretakers of the mosque would act as travel agents for those willing to go to Syria.

"They even raised funds for those who did not have the money to go, so they can depart for Syria."

For months, Mr Bhakti and his team have sat in mosques and Koran reading groups under the cover of being like-minded worshippers and documented the discussions and sermons.

"We are members of their Koran reading groups, we join their activities, we had interviews with congregations, so we obtained information in many ways," he said.

"We observe it ourselves or through our sources and the interviews that we conducted."

IS meetings have gone underground

Mr Bhakti said at times audio recordings of the radical teachings were captured but they could not be given to the ABC as they were the property of the Indonesian Government.

In February last year, the ABC exclusively filmed at the As-Syuhad mosque in central Jakarta as an Islamic State recruitment drive was underway.

Islamic State group sympathisers gave an address to Jakarta's As-Syuhada mosque in Jakarta in February last year. ( ABC )

It would be almost impossible for that to be replicated now, with the groups operating more secretively and sometimes from private homes, according to Mr Bhakti.

In the research he has identified three types of mosques:

Public mosques used by the IS sympathisers without the knowledge of the caretaker

Public mosques used by the IS sympathisers without the knowledge of the caretaker Mosques where the caretaker is linked to IS-affiliated groups but the worshippers are not

Mosques where the caretaker is linked to IS-affiliated groups but the worshippers are not Private mosques where the caretaker and the congregation both support the IS terrorist group

"For radical groups meeting face to face is very important to them because they build their trust after they meet face to face," Mr Bhakti said.

"They can't do that online, online they could be anybody."

Mosque denies preaching IS message

In the city of Bogor, just 55 kilometres south of the capital Jakarta, the ABC travelled to the Ibnu Mas'ud mosque to question the radical teachings.

The mosque is one of the 16 confirmed as preaching the Islamic State ideology. Three of its workers were arrested in Singapore this year and deported home after allegedly trying to reach Syria.

"People can accuse us, but here we do not recruit or send people there [to Syria]," said the mosque's spokesman Jumadi, who goes by one name.

Ibnu Mas'ud mosque, which has a school, denies preaching the Islamic State ideology. ( ABC News )

Jumadi also runs the connected Islamic boarding school for up to 250 students.

"Go ahead, people can accuse us of anything connect us to anything because they all have vested interests," he said, allowing the ABC to walk through and film in the boarding school.

"The local police chief came and checked out this place, we're just a regular boarding school."

But according to Mr Bhakti, the school is training future terrorists.

And he is concerned that as the larger mosques are exposed, the groups are splintering using smaller less obvious prayer groups to spread the dangerous IS message.

Australia calls for cooperation to address terror threat

At the Al Jihad mosque in the town of Bukittinggi in West Sumatra, the ABC had been told preaching has moved to a nearby home after the caretaker was arrested for sending people to Syria.

"They moved to smaller mosques or smaller Koran reading groups, which we call satellite mosques or satellite places," Mr Bhakti said.

"So the number [of mosques] could be bigger."

George Brandis says Indonesia and Australia need to work closely together to tackle terrorism. ( ABC News )

On the weekend in Manado in north Sulawesi, Attorney-General George Brandis co-hosted a regional summit to discuss ways to counter the threat of returning foreign fighters from the Middle East and the Philippines.

The Senator said the sustained fighting in the southern Philippines city of Marawi posed an immediate threat to Indonesia and a more general threat to the region, including Australia.

"The conflict in Marawi reminds us in the most immediate possible way of the urgency and proximity of the threat that is face by all of us," Senator Brandis said.

In the past three months, Indonesian police have increased terrorism related arrests with more than 35 people detained.

Wife of accused terrorist 'shocked' by allegations

One of those is Adi Jihadi, the brother of the Australian embassy bomber Iwan Darmawan, who is better known as Rois and is on death row in Nusakambangan prison.

From behind bars Rois was instrumental in the planning the terrorist attack in central Jakarta in January 2016.

The ABC tracked down Adi Jihadi's wife in Teluk village in Banten, about a four-hour drive south-west of Jakarta.

Accused Indonesian terrorist Adi Jihadi's wife Heni in July 2017. ( ABC News )

She denied any knowledge of her husband's terrorism plans.

"Initially I was shocked, of course, because usually I was with my husband every day and he would take me everywhere with him," 35-year-old Heni told the ABC.

"It's really hard but this is what the reality is and I must face it, I must be ready."

Asked if she thought her husband was a terrorist like his brother, she said: "I don't think so."

Editor's note: Adhe Bhakti is not employed by the Indonesian Government.