BBC News
The riot at the Litoral Penitentiary in the city of Guayaquil reportedly began on Friday evening.
Police tactical units who have entered prison buildings have found guns and explosives, reports say.
Nearly 300 inmates have died so far this year in the country’s prisons.
September’s gang-related violence was the worst in Ecuador’s history.
At the time, inmates from one wing of the prison crawled through a hole to gain access to a different wing, where they attacked rival gang members. Hundreds of officers and army soldiers were deployed to regain control of the complex.
The deadly fight, which saw some inmates decapitated, drew attention to the growing influence in Ecuador of transnational crime gangs such as the Mexico-based Sinaloa and Jalisco New Generation cartels.
The latest fighting has also left 25 people injured and follows a smaller armed clash earlier this month in which three inmates were shot dead.
In a short statement posted to Twitter, President Guillermo Lasso offered his condolences “to the families who have lost loved ones” and said new measures were needed to “fight the mafias that profit from chaos”.
Earlier this month in a BBC interview, Mr Lasso insisted that his government was regaining control not only of the prisons but also of areas of Ecuador where drug traffickers had gained a foothold.
He accused previous governments of being “passive” about drug trafficking but warned that rising drug use in the country would take “more than a decade” to tackle.
And he said Ecuador would need international support from neighbouring Colombia, the US and the EU to strengthen its armed forces and police to combat the growing influence of crime gangs.
Ecuador’s prisons are currently accommodating about 9,000 more prisoners than they were designed to hold, officials say. The Litoral Penitentiary was designed for 5,300 inmates but currently holds 8,500.