Yuri Mora, spokesman for Honduras’ national police investigation agency, said the riot broke out at the women’s prison in the town of Tamara, about 30 miles northwest of the capital Tegucigalpa.
Most victims were burned, but there also were reports of inmates shot at the prison.
At least seven female inmates were being treated at a hospital in Tegucigalpa for gunshot and knife wounds, staff said.
“The forensic teams that are removing bodies confirm they have counted 41,” said Mr Mora.
Local media interviewed one injured inmate outside the hospital who said prisoners belonging to the feared Barrio 18 gang burst into a cell block and shot other inmates or set them on fire.
Honduran President Xiomara Castro said the riot was “planned by maras with the knowledge and acquiescence of security authorities”.
“I am going to take drastic measures!” Ms Castro wrote in her social media accounts.
Julissa Villanueva, head of the country’s prison system, suggested the riot started because of recent attempts by authorities to crack down on illicit activity inside prisons and called Tuesday’s violence a reaction to moves “we are taking against organised crime”.
“We will not back down,” Ms Villanueva said in a televised address after the riot.
Gangs often wield broad control inside the country’s prisons, where inmates often set their own rules and sell prohibited goods.
The riot appears to be the worst tragedy at a female detention centre in the region since 2017, when girls at a shelter for troubled youths in Guatemala set fire to mattresses in protest at rapes and other mistreatment at the badly overcrowded institution.
The ensuing smoke and fire killed 41 girls.
The worst prison disaster in a century also occurred in Honduras, in 2012 at the Comayagua prison, where 361 inmates died in a fire possibly caused by a match, cigarette or some other open flame.
