The Islamic State group claimed responsibility for that incident although police denied its involvement.
East Java Police spokesman Sr.
The first explosion took place at Santa Maria Tak Bercela Church.
Televised eyewitness reports suggested that one suicide bomber was a veiled woman with a couple of children in tow.
Photos and videos of the aftermath of the bombings, some of them graphic, spread quickly online, while the East Java Police were still gathering information of what had just transpired in the province's capital, Surabaya, the nation's largest city after Jakarta.
Egypt's Foreign Ministry has condemned "in the strongest terms" Sunday's suicide bomb attacks on three Indonesian churches which left at least 11 people dead.
The bombings were the worst since a series of attacks on churches on Christmas Eve in 2000 killed 15 people and wounded almost 100. The Islamic State group has claimed accountability.
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. A large blast was heard hours after the attacks, which Mangera said was a bomb disposal squad "securing" a remaining device.
Around 40 others were injured in the attacks, which occurred within minutes of each other.
Shattered glass and chunks of concrete littered the entrance of the church, which was sealed off by heavily armed police.
Although the country is majority Muslim in its population, there is a significant population of Buddhists, Hindus and Christians; the latter being specifically targeted in recent months.
The radical Islamist, who had wanted to fight with the Islamic State group in Syria, injured four people.
The most serious incident was in January 2016 when four suicide bombers and gunmen attacked a shopping area in central Jakarta.
No Malaysian has been affected by the deadly bombings in Surabaya this morning, a Malaysian embassy spokesman said.