One of the most high-profile recent cases was a false claim that went viral last month that China was seeking to wage biological warfare against Indonesia.
The Chinese embassy issued a statement saying the reports were “misleading”.
Indonesian President Joko Widodo appointed Major General Djoko Setiadi, former chairman of the encryption body, to run the organisation.
Setiadi is being called to stifle terrorist networks which communicate online and combat internet hate speech that has been accused of undermining Indonesia’s religious pluralism.
The BSSN faces challenges, including bureaucratic competition, inter-agency coordination, lack of human resources, technology and funding. There are also fears of politicisation amid local elections this year and a general election in 2019.
The elections are seen as likely to compound cyber challenges.
“We will control cyberspace,” Setiadi said.
“Our technology will not only be able to detect, but also to penetrate [extremist] groups,” added Setiadi, from Surakarta, who headed the National Encryption Agency for seven years.
The new body will have to coordinate with the military, National Intelligence Agency, National Counter Terrorism Agency and National Narcotic Agency.
Chairman of a House of Representative commission that will work with the BSSN Abdul Kharis Almasyari said coordination was key.
“The current condition demands the agency to work immediately in synergy with all institutions related to cybersecurity demands. I hope the BSSN can protect crucial sectors in the country,” Almasyari said.
The Justice and Prosperous Party member said the BSSN must remain apolitical and focussed on the national interest.
“I am sure that as we approach the legislative and presidential elections, cybersecurity challenges will become more dynamic and will need better handling,” he added.
The agency must be able to protect infrastructure, including public sector data, finance and transport, from domestic and international hackers, Almasyari said.
Last week, Indonesia said it was appointing an extra 600 staff to its counter-terrorism police to track down groups linked to so-called Islamic State and other extremists.
The 2002 Bali bombing that killed 202 people, mostly foreign tourists, was Indonesia’s worst terror attack.
Subsequent operations weakened most of the Islamist networks but the emergence of Isis has proved effective at creating new radicals.
Indonesia’s police are braced for a busy two years. Picture credit: Wikimedia