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Inmates at La Modelo prison planned the escape attempt as inmates across the country protested overcrowding and poor health services during the COVID-19 outbreak.
Colombia's Justice Minister Margarita Cabello also said the riot injured 83 prisoners Sunday. Cabello added that 32 prisoners and seven guards were hospitalized, and two guards were in critical condition.
The Justice Ministry was investigating the incident.
Cabello said inmates at prisons across the country planned the protests, as 13 other facilities reported disturbances, the BBC reported.
Cabello denied that conditions were unsanitary amid the outbreak, saying, "There is not any sanitary problem that would have caused this plan and these riots."
She also asserted, "There is not one infection nor any prisoner or custodial or administrative staffer who has coronavirus."
Relatives gathered outside the gates of La Modelo prison as they awaited news about their loved ones. They said they heard shots fired when security forces arrived. Videos on social media showed inmates setting fire to mattresses.
Colombia’s 132 prisons had a total inmate capacity of 81,000 but have held over 121,000 prisoners, according to justice ministry figures.
So far, Colombia has reported 231 confirmed cases of coronavirus and two people have died.
The country is set to launch a nationwide quarantine on Tuesday which is expected to last 19 days.
With the exception of medical staff, security forces, pharmacy and supermarket staff, people in the country will be ordered to remain in their homes, officials said. People over the age of 70 have been told to stay indoors until the end of May.