Indonesian jihadists returning from the Syrian civil war could pose a national security threat, Indonesia's counterterrorism chief has warned.

Jihadists coming home from Afghanistan formed radical and terrorist groups, according to National Counterterrorism Agency (BNPT) head Ansyaad Mbai, and history could repeat itself.

"We fear they also may have been trained in Syria. We need to anticipate that upon their return. We should learn from our own bitter experiences of the past," he told Khabar Southeast Asia, adding that his agency would monitor the movements of newly returned Syrian war veterans.

According to the Ministry of Foreign Affairs, some 50 Indonesian militants are in Syria.

"We (got) the information from the Syrian intelligence, but we still can't confirm their whereabouts as they may have taken a non-procedural way to enter the country," Tatang Budi Utama Razak, the ministry's director of legal aid and protection for Indonesians abroad, told Khabar.

Responding to Syria veterans

The impact of returning jihadists will depend on many factors such as ideology and how communities respond to the Syrian veterans, former Indonesian Police Chief Da'i Bachtiar said.

The government could reach out to jihadists under BNPT surveillance and recruit them as part of a non-violent jihad to help develop the country, he suggested.

"Prevent them from being unemployed; get them involved in skilled job training or recruit them to work in accordance with their skills," Da'i told Khabar.

Central Jakarta cleric Muhammad Sutoyo called on fellow Muslims to be vigilant and not allow homecoming extremists to import their brand of jihad from Syria.

"Muslims have different interpretations of 'jihad'. However, we all must recognise that Islam teaches us to be tolerant and to love others. Therefore, whatever happened in Syria should not be brought home," he told Khabar.

Jemaah Islamiyah active in Syria: report

A recent report by the Jakarta-based Institute for Policy Analysis of Conflict (IPAC) examined Indonesian jihadist involvement in the Syrian conflict.

"As far as we know, the number of Indonesian combatants is still in the dozens, but it could climb," IPAC Director Sidney Jones said in a statement accompanying the report's January 29th release. "Jihadi humanitarian assistance teams now appear to be facilitating the entry of fighters as well."

Riza Fardi, also known as Abu Muhammad al-Indunisi, was killed in Syria last year, the report noted. Riza, from West Kalimantan, graduated from the Al-Mukmin Ngruki Islamic boarding school in Solo.

The most active Indonesian group in Syria is Jemaah Islamiyah (JI), which was responsible for the 2002 Bali bombings. Between late 2012 and January 2014, JI's humanitarian arm, the Hilal Ahmar Society of Indonesia (HASI), sent ten delegations to Syria to deliver medical aid and cash to the Islamic resistance, the report said.

"The danger remains that fighters returning from Syria could infuse new energy into Indonesia's weak and ineffectual jihadi movement," the IPAC study concluded.