The country's prison population has more than doubled in the past decade alone, making it the world's fourth-largest with 660,000 prisoners.
"This was one more chapter in the silent and imperious narcotrafficking war", Fontes said at a news conference.
Brazil's prisons are often under the de facto control of drug gangs, whose turf wars on the outside are also fought out among inmates.
Authorities were counting the prisoners to determine how many had escaped.
When the riot started on Sunday afternoon, six headless bodies were tossed over the perimeter fence of the Anisio Jobim Penitentiary Centre, the largest prison in the state.
Brazil's prisons have been criticised by worldwide watchdogs for overcrowding, and violent riots are frequent.
The Anisio Jobim prison complex now houses 2,230 inmates despite having a capacity of only 590.
BEAUTY DEAD IN JAIL MASSACRE Stunning model killed on visit to Guatemala prison during riot in which four people were... "Our prisons were built to annihilate, torture and kill".
Carmelo Anthony Ejected For Hit On Thabo Sefolosha
But the offense definitely suffered, and it's ludicrous to pretend they're more unsafe with Lance Thomas in there than Anthony. This is only their second loss when leading after the fourth quarter this season, bringing their record to 14-2.
The riot in Manaus is the latest clash between inmates aligned with First Capital Command (PCC) gang and a local criminal group known as the North Family.
The FDN is an ally of the Red Command (CV), a gang from Rio de Janeiro that is a rival of the PCC.
Security analysts say a truce that held for years between the PCC and CV broke down last year.
The OAB assisted the inmates with the negotiations and worked to get the 12 hostages taken during the riot released.
Em Tempo newspaper reported that several decapitated bodies were thrown over the prison wall.
Brazil's prison system is precariously overcrowded and conditions in many institutions are horrific.
Brazil has struggled for years against a lucrative and violent drug trade. She said it's been very hard for states to receive funding help for prisons from the central government.