Firefighters battled to extinguish flames while smoke billowed from the compound on the outskirts of the capital Jakarta.
Red Cross officials evacuated victims to ambulances and dozens of bodies in bags were laid in a room at the Tangerang prison.
Detectives in Jakarta are investigating the cause of the fire, which started about 1.45am. Evidence pointed to a short circuit in one of 19 cells in prison Block C2, which was stuffed with 122 prisoners.
Most of the 41 killed were drug convicts, including a man from South Africa and another from Portugal.
A terrorism convict and a murder convict were also killed, according to Indonesia‘s Justice and Human Rights minister Yasona Laoly.
He expressed his deep condolences for the victims’ families and pledged to provide the best treatment for those injured.
“This is a tragedy that concerns all of us,” Mr Laoly said.
“We are working closely with all relevant parties to investigate the causes of the fire.”
Hundreds of police and soldiers were deployed around the prison to prevent inmates from escaping after the flames were extinguished.
Police Chief Fadil Imran said: “The situation is now under control.”
Eight people were hospitalised with severe burns and nine with light injuries were treated at a prison clinic.
Another 64, many suffering smoke inhalation, were evacuated to a mosque in the compound.
Tangerang prison was designed to house 1,225 inmates but has more than 2,000, according to a spokesperson for the corrections department at the Justice Ministry.
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