Few details including the deceased man's identity and the motive for the kidnapping were released. A spokesperson for the Houston bureau of the FBI was not immediately available for comment.
The victim was abducted from his home Wednesday in Conroe, Texas, a suburb 40 miles (64 km) north of Houston, the paper reported. He was held in a home in the city's Trinity Gardens neighbourhood, media reports said.
The Chronicle reported that the man's brother was called on the phone by someone claiming to be with a cartel and asked to pay a ransom, and the police and FBI were alerted.
Two men and one woman were arrested on felony kidnapping and other charges and the investigation is ongoing. The FBI agent who shot the man was placed on administrative leave, Garza said at a press conference, media reports say.
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