Flores, the commander of state investigators in Ciudad Miguel Aleman who was part of a group investigating the reported shooting of David Hartley, was killed, said Ruben Rios, spokesman for the Tamaulipas state prosecutor's office.
U.S. officials have said threats from drug gangs who control the area around Falcon Lake have hampered the search for Hartley.
Hartley's wife, Tiffany, says she and her husband were attacked by pirates on the lake on Sept. 30, while they were returning to the United States from Mexico on Jet Skis. Hartley was shot and presumably fell into the lake.
Lesley Lopez, a spokeswoman for U.S. Rep. Henry Cuellar, who has been involved in the investigation, said U.S. authorities were "slightly concerned that it was someone who was working as a U.S. ally on this case."
U.S. officials, particularly Texas Gov. Rick Perry, and Hartley's family have been pressuring Mexico to step up the search for Hartley and determine what happened.
Fred Garza, chief deputy sheriff in Webb County, on the Texas-Mexico border, said the search was continuing Tuesday.
Perry was expected to comment later Tuesday.
Falcon Lake is a dammed section of the Rio Grande, 25 miles long and 3 miles across. Pirates have robbed boaters and fisherman on the Mexican side, prompting warnings to Americans by Texas state officials, but Hartley's death would mark the first violent fatality on the lake.
Tiffany Hartley said men on three speedboats fired on her and her husband as they were riding Jet Skis back from a trip to Tamaulipas to photograph a half-submerged church, and that her husband was shot in the head. She said she tried to retrieve his body and his Jet Ski but the pirates continued firing and she fled to the U.S. side. Zapata County, Texas, Sheriff Sigifredo Gonzalez has said he has an eyewitness who corroborates her account.
Dennis Hartley, David Hartley's father, expressed shock and regret at Flores' killing.
"I just, I'm in shock about this right now," he told The Associated Press from his Colorado home. "I really don't have any hope that David will be found. I really hate other people putting their lives at stake. We don't need more sons lost. If this is true, I'm just really heart broken that this happened."
The Mexican Foreign Ministry says it has been using federal, state and local resources, including the military and helicopters, to search for Hartley's body and opened an investigation. Over the weekend, authorities named two possible suspects.
That part of Tamaulipas state is overrun by violence from a turf battle between the Gulf Cartel and the Zeta drug gang, made up of former Mexican special forces soldiers, and both are battling the Mexican military.
Last week, Perry said he expected Mexican President Felipe Calderon to call him within 48 hours to report a body had been found and that even the threat of drug gang violence against search crews was no reason to halt the efforts.