Some of the prisoners involved in the clashes are Islamist militants jailed on terror-related charges, according to police.
Authorities were unsure how many people remained inside the prison complex.
Negotiations were underway for the release of the hostage, said national police spokesman Muhammad Iqbal.
The Islamic State group's Amaq News Agency said its fighters took part in the riot late Tuesday.
Mr Iqbal denied IS was behind the attack or that it had been planned.
In an interview with MetroTV station, police spokesman Setyo Wasisto said the inmates who provoked the riot were members of Jemaah Anshorut Daulah, a network of Indonesian extremist groups formed in 2015 that pledges allegiance to Islamic State group leader Abu Bakr al-Baghdadi.
Chief security minister Wiranto said the incident was being treated "very carefully because it concerns national security".
The ABC has confirmed five police officers and one inmate have been killed, and another police officer is still a hostage.
An armored vehicle is parked outside the headquarters of Mobile Brigade, an elite Indonesian police force, following a riot at the detention center inside the compound in Depok, West Java, Indonesia, Wednesday, May 9, 2018.
Police were negotiating with the prisoners, he said.
"If they surrender, it will be a non-violent process". He said a dispute had broken out late on Tuesday with prisoners who objected to authorities making checks on their food.
"We have isolated them into one block, so the situation is under control", General Iqbal said. The jail holds around 130 convicted terrorists, Reuters reports.
Situation in jail holding ISIL suspects near Jakarta tense as police officers continue to be held hostage by inmates.
Last year, an attack by two suicide bombers, using pressure cookers packed with explosives, killed three police officers and wounded 12 at a Jakarta bus terminal.
In January 2016, four Islamic State-linked militants mounted a gun-and-bomb attack at an intersection outside a Starbucks cafe in central Jakarta, killing themselves and four others.