[39] The attacks, and subsequent travel warnings issued by other countries, severely damaged Indonesia's tourism industry and foreign investment prospects.

[40] However, after the capture and killing of most of its key members and leaders, most notably Imam Samudra, Amrozi, Abu Dujana, Azahari Husin, and Noordin Mohammad Top, the terrorist cells in Indonesia have become less significant.

On 15 April 2011 a suicide bomber detonated an improvised explosive device in a mosque in a police compound in the city of Cirebon, West Java, during Friday prayers.

On 8 April 2012, a Trigana Air PK-YRF airplane was shot at by unidentified gunmen during a landing approach on Mulia airstrip, Puncak Jaya, Papua.

[44] On 27 November 2012, three policemen stationed at the remote Pirime police post, Jayawijaya, Papua, were killed in an attack by a group of unidentified men.

The Jakarta bombings and legal prosecutions helped shift public opinion away from the use of extremist Islamic political violence, but also increased the influence of intelligence bodies, the police and military whose strength had diminished since 1998.

[47] The attacks, and subsequent travel warnings issued by other countries including the United States[48] and Australia,[49] severely damaged Indonesia's tourism industry and foreign investment prospects.

Formed after the 2002 Bali bombings, the unit has had considerable success against the jihadi terrorist cells linked to the Central Java-based Islamist movement Jemaah Islamiah.

On 9 November 2005, bomb expert and senior player in Jemaah Islamiyah, Malaysian former university lecturer Dr. Azahari Husin, along with two other militants were killed in a raid on a house in Batu, East Java.

The police stated that it was committed by a more radical splinter group of JI, led by the man then dubbed as the most wanted terrorist in Southeast Asia, Noordin Mohammad Top.

[56] On 9 March 2010, Dulmatin, a senior figure in the militant group Jemaah Islamiyah (JI) and one of the most wanted terrorists in Southeast Asia was killed in a police raid in Pamulang, South Tangerang by Detachment 88.

Since then, the JAD (Jamaah Ansharut Daulah), JI (Jemaah Islamiyah), has been submitted as active terrorist groups in Indonesia, which membership to either of these organisation will be prosecuted immediately by Indonesian law.