No one has yet claimed responsibility for the Sunday bombings in Indonesia's second-biggest city Surabaya.
According to The Straits Times, the police chief of the province of East Java General Arifin Mahfoud told reporters that according to preliminary investigations, the attacks were made by suicide bombers who used to attack motorcycles or cars.
The number is expected to rise.
"The victims are still being identified", Frans Barung Mangera, East Java police spokesman said on Sunday.
"We have confirmed one died at the scene, one died at the hospital, two police officers were injured and there are some civilians injured", Mangera said.
Television footage showed one church engulfed in fire, with thick, black smoke billowing up.
Authorities were also investigating whether there was an explosion at a fourth church. The Daesh terror group had claimed responsibility.
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He said two police officers were among a total of 40 wounded.
Indonesia is home to significant numbers of Christians, Hindus and Buddhists but there are concerns over rising intolerance.
Indonesia, the most populous Muslim-majority country, has seen a resurgence of Islamist militancy in recent months.
A sustained crackdown weakened the most risky networks but the emergence of IS has proved a potent new rallying cry for radicals.
Hundreds of Indonesians have flocked to fight with ISIS, sparking fears that extremist outfits could get a new lease on life.
Churches have also been targeted previously, including near-simultaneous attacks on churches there at Christmas in 2000 that killed about 20 people.