Over 90 prison guards are being held hostage by inmates across five separate prisons in what has been described as a "state of emergency".
Ecuador's government confirmed the emergency in two provinces over the weekend which erupted when a mayor was killed and prisoners in five jails carried out an uprising.
Hundreds of inmates have been killed over the last few years as members of competing criminal organisations fought off against one another inside and out.
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But prison clashes over the last few days left six dead, with the city of Manta, where mayor Agustin Intriago was killed, is under a 60-day lockdown.
Confirming the attack on Twitter, president Guillermo Lasso condemned the gruesome killing and said he "ordered the general commander to activate the necessary resources".
His aim in granting military powers for the next 60 days is so the "people responsible for this crime are found and brought to justice."
He also offered his thoughts to the family of the mayor and of other victim Ariana Chancay, who was also killed in the attack which left four others injured.
The cocaine transit point was peaceful up until a decade ago, CNN reported, with the United States and Canada seeing an influx of cocaine through the country.
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Since then, president Lasso has faced an impeachment vote and a dissolved congress, with a snap election planned for August 20.
Manta will stay in its state of emergency and curfew for 60 days, as will the province of Los Rios and Duran, which are to be under strict rule until the two-month period is up.
It comes as prisoners take at least 90 prison guards hostage, usurping the power structure inside five of the biggest prisons in Ecuador and sparking outrage from the government.
Inside the prisons, at least six people were killed in recent days, a report from penitentiary service SNAI confirmed.
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