The clashes took place in a ward with 700 prisoners in the Litoral security prison in the coastal city of Guayaquil.
According to the police, conflicts flared up between different groups as a result of a person who had a leading role in it being released.
The death toll was first reported to be just over 50 people.
But after a few hours, it had risen to at least 68. The information came from Ecuador's prosecutor's office, writes AFP.
Lasted for hours
Residents nearby said gunshots and explosions were heard from the jail for hours.
According to the Ecuadorian newspaper Expreso, police who intervened found a rifle and dynamite in the department.
The newspaper reported early on what happened, as several prisoners had broadcast the course of events live on social media.
In a similar settlement in the prison, 118 people were killed.
The clashes that erupted on September 28 concerned conflicts between rival gangs that are considered to have close ties with Mexican drug cartels.
Crowded prisons
Only when the police and military were deployed, a total of 900 men, could order be restored.
President Guilllermo Lasso was forced to declare a state of emergency to regain control.
This year alone, nearly 300 people have been killed in prison riots in Ecuador.
About 40,000 prisoners are in the country's overcrowded prisons.
The prison complex in Litoral alone has 8,500 prisoners.