Paulo Malhaes, 76, was killed by three men who entered his home outside Rio de Janeiro on Thursday, police say.
Last month, Paulo Malhaes said he never regretted killing “as many people as necessary” and tortured “many” prisoners.
Almost 500 people disappeared or were killed in Brazil when it was ruled by the army between 1964 and 1985.
Thousands more were detained and tortured, including current President Dilma Rousseff.
According to his wife, Col. Paulo Malhaes was suffocated by three men who broke into their home. Police say the assailants stole computers and some guns.
Prominent Brazilian lawyer Wadih Damous said the intruders may have been after secret files he held.
Last month Col. Paulo Malhaes appeared before Brazil’s National Truth Commission, which is investigating past abuses.
He gave testimony on how he had tortured many political prisoners.
“I did my duty. I have no regrets,” he told the commission.
He defended his actions saying that the people he killed and tortured were “guerrillas who fought an armed struggle”.
Brazilian police say they are looking for CCTV images which might help identify Col. Paulo Malhaes’ killers.
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