The attacks occurred within minutes of each other, according to Surabaya police spokesman Frans Barung Mangera.
However, Wawan Purwanto, communication director at Indonesia's intelligence agency said ISIS-influenced group Jemaah Ansharut Daulah (JAD) is suspected of being behind the bombings, Reuters reported. The Islamic State (ISIS, according to its acronym in English) has claimed authorship of attack.
"We are angry", association official Gormar Gultom said, but urged people to let the police investigation take its course.
In line with Karnavian's chronology of occasions, which does not line up with the sequence Mangera beforehand supplied to the state-run Antara news agency, the daddy, recognized as Dita Sopriyanto, drove a van to the Indonesian Christian Church and dropped off spouse Puji Kuswat and their 9- and 12-year-old daughters.
One suicide bomber appeared to have been disguised as a churchgoer.
"D then drove the auto containing bombs to the Pentecostal Church and blew it up".
On the similar time, the final stated, Sopriyanto's sons drove bikes to Santa Maria Catholic Church, the place they, too, detonated bombs.
Karnavian said Sunday's attacks may have been revenge for the arrest of some of JAD's leaders and for the prison crisis which eventually saw the surrender of the radical inmates.
Police have closed all three areas as they examine.
"All were suicide attacks but the types of bombs are different", he said. A bomb squad carried out a managed explosion of the gadgets, he stated.
The investigators also found "black powder" at the homes, and officers seized books and documents from the house, Setiawan said.
Pope Francis offered his prayers for the victims.
"Together we invoke the God of peace (asking him) to cease these violent actions and (to make sure) that in the heart of all there could be a space for feelings not of hatred and violence but of reconciliation and fraternity".
"No words can describe how deep our condolences are for the fallen victims".
The first church attack occurred at 7:08 a.m.
"These assaults on peaceable worshipers are an affront to the tolerance and variety embraced by Indonesians".
Almost 90 per cent of Indonesia's 260 million people are Muslim, but there are significant numbers of Christians, Hindus and Buddhists.
President Joko "Jokowi" Widodo arrived in Surabaya, the East Java provincial capital, in the aftermath of the attacks, Mangera said.
Indonesia is the world's most populous Muslim country. More than 82% of its roughly 261 million people observe Islam. Nearly 10% of the population is Christian. Sunday's attacks were the deadliest to target Christians since a series of bombings on Christmas Eve in 2000 killed 15 people and injured almost 100 others.
In recent years, Indonesia has been confronting ISIS attempts to recruit members in the country.
The attacks are the worst in Indonesia since October 2005, when three suicide bombers blew themselves up in Bali restaurants, killing 20 people, including many foreign tourists. Authorities suspect ISIS involvement.
Sunday's bombings had the highest death toll since nine people were killed in 2009 attacks on two luxury hotels in Jakarta.