Deputy Interior Minister Jose Luis Quiroga said the six dead at the Palmasola prison were inmates "who resisted the police incursion."
Police said five police and 18 inmates were injured in the operation, which was launched to search the prison for weapons and drugs in the wake of a riot.
About 2,000 police surged into the cell blocks before dawn, a week after an uprising triggered by a government order that bars children younger than six from visiting jailed relatives.
Police chief Alfonso Mendoza said the search turned up "a still to make alcohol, and endless stands for sales of drugs, marijuana, cocaine."
"There was complete lawlessness in Palmasola," he said.
Inside the prison, the situation was relatively calm after the operation, but outside, police clashed with people wanting to know the fate of their relatives.
Located in eastern Bolivia, Palmasola is reputed to be one of the most dangerous and overcrowded penitentiaries in the country.
Bolivian prisons have capacity for 3,730 inmates, but hold more than 15,000, according to official figures that date from December 2016.
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