Televised eyewitness reports suggested that one suicide bomber was a veiled woman with a couple of children in tow.
The St. Maria explosion killed four people and two people were killed at each of the other two churches, the spokesman said.
The first attack struck the Santa Maria Roman Catholic Church in Surabaya, killing four people, including one or more bombers.
This is a developing story.
"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 images showed toppled motorcycles and debris scattered around the entrance of one church and police cordoning off areas as crowds gathered. There were no immediate claims of responsibility, but religious violence and tensions have been rising throughout this predominantly Muslim country. The Islamic State group has claimed accountability.
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Wawan Purwanto, communication director at Indonesia's intelligence agency said Islamic State-inspired group Jemaah Ansharut Daulah (JAD) was believed to be behind the bombings.
The blast was followed by a second explosion minutes later at the Christian Church of Diponegoro and a third at the city's Pantekosta Church, police spokesman Frans Barung Mangera said.
"PGI is concerned because this had happened many times and often taken place around the time of Sunday services", said Jeirry Sumampow, a spokesman for the Indonesia's Communion of Churches.
Hundreds of Indonesians have flocked to fight with IS, sparking fears that extremist outfits could get a new lease on life. The incident is estimated to be the deadliest attack in recent years to hit the world's biggest Muslim-majority nation.
As of 10.30 a.m., police reported that at least nine people had been killed, while at least 40 had been injured in the attacks.