The Southeast Asian nation, which will begin the holy fasting month Ramadan this week, has been on high alert over attacks by homegrown militants, including some incidents claimed by the Islamic State group.
No one has yet claimed responsibility for the Sunday bombings in Indonesia’s second-biggest city Surabaya.
“Nine people are been killed and 40 are in hospital,” East Java Police spokesman Frans Barung Mangera told reporters, adding that two police officers were among the injured.
The official death toll climbed from an initial two killed and may include those who succumbed to injuries in hospital.
Three separate locations were hit by the bombings around 7:30 am (0030 GMT) in what appeared to be coordinated attacks that included suicide and possibly vehicle bombings.
Police bomb experts were called in to disarm still active explosives at the Gereja Pantekosta Pusat Surabaya (Surabaya Centre Pentacostal Church), with an AFP reporter at the scene hearing two loud explosions.
Images from one scene showed a body lying outside the gate of Santa Maria catholic church and members of Indonesia’s bomb squad poring over the rubble.
At least one of the attackers was killed when they detonated their bomb at Santa Maria. It was not clear if any other perpetrators were among those killed or injured.
“I was frightened… many people were screaming,” 23-year-old witness Roman told AFP after the blast at Santa Maria church.
Police guarded a Sunday mass at another church in the city of Bandung, between the capital Jakarta and Surabaya where the bombings happened.
The attacks started coming several days after five Indonesian police officers and a prisoner were killed in clashes that saw Islamist inmates take a guard hostage at a high-security jail on the outskirts of Jakarta.
The Islamic State (IS) group claimed responsibility for that incident although police rejected its involvement.
Indonesia’s 260 million people includes significant numbers of minority Christians, Hindus and Buddhists but there are concerns over rising sectarian intolerance and militancy.