In the early hours of Saturday, some 1,000 officers lined up and patrolled the grounds in a bid to gain control of the Zonal 8 prison.
According to the police, the agents were met with gunshots by the inmates, but they immediately managed to neutralize the action.
Authorities said at least four inmates were injured, and rifles and bullets were seized during the operation.
Dozens of inmates' relatives have gathered outside prison seeking information about their loved ones. Relatives were seen crying and praying next to the prison.
This week Ecuador reported a prison riot at the Penitenciaria del Litoral, which left more than 100 people were killed and 80 injured in the most deadly act of violence ever reported in the country's prison system.
Ecuador has been the scene of bloody fights between gangs for control of the prison in recent months.