Ecuadorean authorities on Tuesday lowered the death toll to 62 from violence at the Penitenciaria del Litoral prison over the weekend, but said areas of the facility remain out of their control.
The government has blamed bloody confrontations at the prison, located in the city of Guayaquil, on gang competition to control jails and drug trafficking routes.
In September, 119 people were killed in a similar incident of violence at the same prison, which is the country's most violent.
The national government and the attorney general's office said over the weekend that 68 prisoners were killed in overnight violence that began on Friday. But the police said on Tuesday that just 62 bodies were sent to the morgue for identification.
"We received 62 bodies, of which 46 have been identified already and 34 turned over (to their families)," the police's national director for scientific investigation, Marco Ortiz, told Reuters.
"There are bodies that have been dismembered, so the 18 anatomical parts found at the time would correspond to them," he added.
President Guillermo Lasso said on Monday that Ecuador - which has long faced criticism for overcrowded and unsanitary conditions at detention centers - would confront the prison crisis with a "pacification process" among rival gangs, a military presence and legal reforms.
Ecuador will seek assistance from allies like the United States and Colombia to fight international drug cartels, Lasso added, alleging they operated without resistance in the Andean country until he took office in May.
More than 1,000 security personnel entered the penitentiary on Monday and three prisoners kidnapped by fellow inmates have been freed, the government said.
But some parts of Litoral remain outside of security force control, the head of prison authority SNAI told local media.
"We've still to take control of the cellblocks," said Fausto Cobo. "The main thing now is to recover control. If the security forces don't do it, no one will."