Commander Rolando Flores was looking into the disappearance of David Hartley, who is from Milliken, Colo. He was in the border city of Ciudad Miguel Aleman.
Ruben Rios, spokesman for the Tamaulipas state prosecutor's office, said Flores "unfortunately was killed."
Rios said authorities "don't know how or why he was killed. We don't have any details on how he died."
David Hartley was apparently shot and killed on Sept. 30. Hartley and his wife Tiffany were jet skiing on Falcon Lake, which is on the U.S.-Mexico border. Tiffany Hartley got away.
U.S. officials have said threats from drug gangs who control the area around Falcon Lake have hampered the search for Hartley.
Flores' head was delivered to the Mexican military in a suitcase.
Authorities say his murder was unrelated to the Hartley investigation.
Others disagree with that assessment.
"I would assume he was killed because he was either trying to assist in the rescue operations in the search operations or because he may have provided some documents to the media from what I understand," Zapata County Sheriff Sigifredo Gonzales said.
A local television station in Brownsville, Texas says Flores was their source on a story about suspects in David Hartley's killing.
"We've always known that the cartels really control what's happening in Mexico to a certain extent. It's very obvious with what happened here if you're involved with trying to perform some type of rescue operation, or search operation, your life is in danger, simple as that," Gonzales said.
The Hartley family has pushed Mexican authorities to help in finding and returning David Hartley's body.
On Monday, David Hartley's father, Dennis, told 9NEWS he did not think his son's body will ever be returned.
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."
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, Texas Gov. Rick Perry had 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.
David's mom, Pam, Tiffany Hartley, and her parents, are still in McAllen, Texas near the border. There is no word on when they'll return back to Colorado.
(KUSA-TV © 2010 Multimedia Holdings Corporation with The Associated Press)