Mr Iqbal denied IS was behind the attack or that it had been planned.
The Commissioner General of the National Police Syafruddin, said there were no fatalities during this operation which resulted in the surrender of about 150 prisoners.
"Six of them were our colleagues and one victim was an inmate we were forced to neutralize as he attempted to grab an officer's weapon", national police spokesman Muhammad Iqbal told reporters.
The Islamic State group's Amaq News Agency published a report after the riot broke out saying the melee was between its fighters and the counterterrorism squad.
He revealed that a total of 156 terrorist inmates allegedly got involved in the clash, most of whom have surrendered and will soon be transferred to other prisons.
Several blasts heard near the prison on Thursday morning were caused by police destroying home-made bombs created by the prisoners, police said.
The riot began on Tuesday night when the guards refused to give an inmate food brought by his family which led the prisoner to urge other inmates to revolt, according to officials.
"It is quite ironical that while the chief of the Indonesian police is in Jordan to open an exhibition and speak of Indonesia's success in combating terrorism, a riot has broken out at the Brimob detention center and killed five police officers have been killed", he explained. He is on trial for terrorism and is held at the same prison. Police officers maintained tight security around the jail and kept onlookers away from the entrance.
Islamic State sympathisers have carried out a series of mostly low-level attacks in Indonesia over the past few years.
Last year, an attack by two suicide bombers, using pressure cookers packed with explosives, killed three police and wounded 12 at a Jakarta bus terminal.