The Indonesian government is taking steps to counter the radicalisation of mosques in Jakarta by deploying plainclothes officials to find out who manages them and what they preach.

A member of the government task force told The Straits Times that they have already uncovered an alarming fact - that some mosques in high-rise office buildings on the main Thamrin and Sudirman roads of downtown Jakarta, and just minutes from the presidential palace, are run by white-collar staff who are radicals.

At least one major government ministry and a top engineering school in Bandung, West Java, are also managed by radical groups. The government will now firmly "encourage" the building owners to oust the radical mosque caretakers.

The source told ST on Wednesday: "Typically, these mosques were rarely frequented - as we say the least 'makmur' mosques - so dedicated, radical Muslims were moved and began to dominate their day-to-day running and assumed the caretaker's role."

So committed are these new caretakers - some of whom are university graduates - that they invited hardline preachers to give sermons, he said.

The chairman of Indonesia's largest Islamic organisation Nahdlatul Ulama, Mr Said Aqil Siradj, told reporters on May 23 that radicalism has spread to mosques in a number of prominent universities in Jakarta, and the government needs to take urgent action to keep this from happening.

Mr Said Aqil also appealed to the government to be more active in countering the spread of radicalism on social media. He said he often noticed provocative sermons posted on Facebook that deviated from mainstream Islamic teaching.

Indonesia, which has the world's largest Muslim population, has seen a rise in Islamism, as rogue political elites in recent years have increasingly taken to rousing religious sentiments and racism to win elections and secure power.

While silent, moderate Indonesian Muslims are by far in the majority, there is a small minority of very vocal radicals who are often influential.

Officials in Indonesia categorise a mosque as radical if the caretaker has some affiliation to, or is a member of, any group that promotes syariah law or the establishment of an Islamic state, such as the Hizb ut-Tahrir Indonesia (HTI), a branch of a global Islamist group that the Indonesian government has filed to court to disband.

Mr Adhe Bhakti, a researcher at the Centre for Radicalism and Deradicalisation Studies, told ST: "Hizb ut-Tahrir Indonesia seeks to establish an Islamic caliphate. This objective is in line with the groups that have been promoting terror (in Indonesia).

"They are only one step towards violence, that is terrorism, because they share the same idea. Those that already engage in terrorism do not believe that not doing so would help them achieve their objective."

Among the terrorists who were members of HTI is Bachrun Naim, a Central Java-born militant who has lived in Raqqa, Syria, where he fought with terror group Islamic State in Iraq and Syria and supervised recent bomb attacks in Indonesia from there.

Another HTI member is Nurul Azmi Tibyani, who in 2013 was jailed for four years and fined 200 million rupiah (S$20,800) for taking part in a cell that managed to hack an e-commerce website and steal 5.9 billion rupiah.

Some of that money was used to fund fellow militants' paramilitary training in Poso, Central Sulawesi, and Indonesia's most wanted terrorist, Santoso, who was killed in a joint police-military raid last year.