Police and bomb squad officers had surrounded the house in Sibolga, North Sumatra, after arresting her husband a day earlier over his suspected links to a planned attack on a local police headquarters. The wife and child had remained in the house.
"Police, religious figures and relatives of the suspect were negotiating with the suspects and asked them to surrender but they still stayed inside," said national police spokesman Dedi Prasetyo.
During a standoff lasting nearly 12 hours, the wife allegedly threw an explosive device at the security forces, wounding a police officer and a civilian.
"At 1.25 a.m. the wife of the terrorist and their son blew themselves up inside the house," Prasetyo said, adding the force of the explosion sent debris flying at least a block away.
Police found about 30 kg of explosives at the site, according to media reports. They did not elaborate on the age of the son.
Authorities believe the husband is part of Jemaah Ansharut Daulah (JAD), the largest Islamic State-linked group in the country, which was legally disbanded last year for "conducting terrorism" and affiliating itself with the foreign militant organisation.
The incident is reminiscent of a series of gruesome attacks in the city of Surabaya last May, when whole families, including children as young as nine, strapped on explosive vests and blew themselves up at churches and police stations, killing more than 30 people.
Islamic State claimed responsibility for the attacks, which prompted the country to toughen up its anti-terror laws. Since then, counter-terrorism police looking to defuse homegrown radicalism have detained hundreds of suspected militants.
Under the revised law, anyone suspected of planning an attack can be held for up to 21 days for an initial inquiry and for up to 200 days for a formal investigation.
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