Five officers and one prisoner were killed on Wednesday in a riot at a police detention centre in a city near Indonesia's capital that authorities allege was earlier being targeted by Islamic militants, officials said.

National police spokesman Muhammad Iqbal told reporters that one police officer remains hostage inside the detention centre.

The riot happened in Depok, on Jakarta's southern outskirts, where four days earlier police arrested three Islamic militants they say planned to attack the headquarters and other police stations in the same town.

The Islamic State group's Amaq News Agency published a report saying the fighting that broke out at the prison late Tuesday was between its fighters and the counterterrorism squad.

Unconfirmed reports said the riot began when some extremist detainees tried to grab weapons from guards on the counterterrorism squad.

The inmates reportedly pushed an iron trellis until broken before taking long-barreled weapons and breaking through the ammunition room inside the detention building.

That led to a shootout between the inmates and counterterrorism officers.

The rioting happened four days after the arrests of three Islamic militants who planned to attack the headquarters and other police stations in the same town.

Indonesia, the world's most populous Muslim nation, has carried out a sustained crackdown on Islamic militants since the 2002 Bali bombings by Jemaah Islamiyah network that killed 202 people, mostly foreigners.

The network was neutralised following the arrests of hundreds of its militants and leaders.

But new threats have emerged recently from Islamic State group-inspired radicals who have targeted security forces and local "infidels" instead of Westerners.