A suspect whose T-shirt had "jihad" on it was arrested soon after a church in Samarinda, East Kalimantan, was hit by a blast which injured four people yesterday.
Police said they had arrested a male suspect in connection with the morning attack and are looking for his accomplice who fled.
Samarinda police chief Colonel Setyobudi Dwiputro told local media that the suspects were on a motorcycle when they threw what was believed to be a low-grade Molotov cocktail or homemade bomb.
The suspect, who was nabbed at a nearby river, was identified only as "J" and appeared to be in his early 20s. Col Setyobudi said "J" was born in Bogor, West Java, but lived in a neighbourhood mosque in Samarinda. According to reports, his face looked injured when he was arrested, although it was not known how he was hurt.
President Joko Widodo called for a full investigation. "The bomb case in Samarinda must be fully investigated. Police will carry out firm law enforcement," he said on Twitter.
There has been a spate of similar attacks in Indonesia this year.
The modus operandi is for one or two young men to strike, often with homemade bombs or improvised explosive devices.
In July, a suicide bomber riding a motorcycle killed himself and injured a policeman when he was prevented from entering a police outpost in Solo, Central Java.
In August, an 18-year-old targeting a church in Medan stabbed a Catholic priest after his bomb failed to detonate.
These cases have prompted the Indonesian authorities to launch a multi-agency deradicalisation effort to reach out to young Indonesians who might otherwise be indoctrinated by extremist teachings, especially those of domestic terror groups loyal to the Islamic State in Iraq and Syria.