The riot broke out in the early hours of Monday over a clash between rival gangs. Some prisoners attempted to escape the facility, with 40 people having been detained near the prison's outside perimeter. Earlier in the day, the death toll stood at 20.
"During the riots... 43 inmates have died," the office said.
More than 100 inmates are now reportedly on the run.
This prison riot is not the first in Ecuador. In early April, clashes in the prison of the Ecuadorian city of Turi in the province of Azuay led to the death of 20 people. In November 2021, 68 people were killed and 25 others were injured during a riot in an Ecuadorian jail in the city of Guayaquil, the same facility where more than 100 died in riots in late September.