It is believed coordinated fights broke out in the maximum-security wings as rival gangs fought for leadership in the centres.
Dozens of inmates have died, with some reportedly beheaded and dismembered, during a series of riots at prisons in Ecuador this week.
Following one of the bloodiest outbreaks of prison violence in the country's history, authorities regained control of the facilities in three cities after raids by hundreds of police officers and military personnel.
According to reports, coordinated fights broke out in the maximum-security wings as rival gangs fought for leadership within the detention centres.
Authorities have said the clashes that began on Monday night were sparked by weapons searches.
The national agency responsible for the prisons said at least 79 inmates had died, including 37 inmates in the Pacific coast city of Guayaquil, 34 in the southern city of Cuenca, and eight in the central city of Latacunga.
The prisons' maximum-security areas tend to house inmates linked to killings, drug trafficking, extortion, and other major crimes.
Deadly prison riots have happened relatively frequently in recent years in Ecuador, whose prisons were designed for some 27,000 inmates but house about 38,000.
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