Around 40 others were injured in the attacks, which occurred within minutes of each other. No group has so far said it carried them out.
TV pictures showed debris scattered around the entrance of one church.
Indonesia, the most populous Muslim-majority country, has seen a resurgence of Islamist militancy in recent months.
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The bombings took place around 07:30 local time (00:30 GMT). Officials said they foiled an attack against a fourth church. The country’s intelligence agency said the attacks were most likely to have been carried out by an Islamic State-inspired group, Jemaah Ansharut Daulah.