Despite the steady weakening of major jihadi groups, the potential for low-tech, low-casualty terrorist violence in Indonesia remains high, facilitated by corruption and other shortcomings in key state institutions. Every arrest of a terrorist suspect — and there were more than a hundred in 2010 — produces new information showing that extremist networks are more extensive than previously thought and that groups are constantly evolving and mutating, with older organizations like Jemaah Islamiyah losing ground to new alliances.

The fact that the only deaths at terrorist hands in 2010 were ten Indonesian police officers highlights an ideological shift among extremists that has been taking place for the last several years: Indonesian officials are now seen as at least as much the enemy as the United States and its allies. That shift has come about partly in recognition of the lack of public support for attacks on foreign civilians, partly through the influence on Indonesian radicals of the Jordanian writer Abu Muhammad al-Maqdisi, and partly out of determination to avenge the deaths of mujahidin killed in police raids.

It has produced a concomitant shift in Indonesian Government thinking. Particularly after a plot was discovered in mid-2009 against President Yudhoyono by the same team that bombed two luxury hotels in Jakarta, the government began to see terrorism as an issue of state security, not just an extraordinary crime. This in turn helped fast-track the establishment in July 2010 of the National Anti-Terrorism Agency (Badan Nasional Penanggulangan Terorisme, BNPT) and has led to a push by the Indonesian military for a greater role in counter-terrorism efforts. The government made little headway during the year in terrorism prevention efforts, but it did acknowlege the need for better prison oversight after some twenty former prisoners were captured or killed in police operations during the year. The recidivists included several common criminals who had been recruited in prison. While plans remain under discussion for constructing a separate facility for terrorists, some steps were taken towards better monitoring of detainees. Several particularly high-profile suspects arrested during the year were isolated from their friends and held in separate police lock-ups while awaiting trial.