The suicide bombings at three churches in Surabaya, East Java were carried out by a family of six, believed to have been involved in a terrorist group.
The family consisted of a man, his wife and four children aged 9 to 18.
Indonesian police chief General Tito Karnavian said the suspects split into three groups before they headed to the churches to detonate the bombs strapped to their bodies.
In the incident which occurred between 6.45am to 7.45am, 13 were reported killed as at 7pm including all suspects, while 41 others were injured.
The suicide bomber at the Central Pentecostal Church in Jalan Arjuna was the head of the family known as Dita Prianto.
Dita had earlier sent his wife and two daughters aged 9 and 12 to the Indonesian Christian Church in Jalan Diponegoro where the trio blew themselves up.
Dita’s two sons aged 16 and 18 were sent to the third location, namely the Santa Maria Tak Bercela Church on Jalan Ngagel Madya.
Antara news agency reported that Indonesia's President Joko Widodo, who visited sites this afternoon, denounced the incident and ordered for tighter security control.
"Terrorism is a crime against humanity which has nothing to do with any religion.
"All religious teachings reject terrorism," said Jokowi.
Indonesian police have also increased security at several areas, including airports, places of worship, and those with a high risk of being attacked.
Meanwhile, a spokesperson for the Malaysian Embassy in Indonesia advised Malaysians in Indonesia to remain vigilant.
No Malaysians were harmed in the incident.