General Ricardo Cesar Nino Villarreal and his wife were killed as they drove Saturday in Vallecillo, in the northern state of Nuevo Leon.
But their two-door car and the bodies were found only Sunday by people who were driving by on the road linking the cities of Monterrey and Nuevo Laredo, said the security task force of the neighboring state of Tamaulipas.
More than 100 high-caliber bullet casings were found at the scene of the shooting, officials said.
Nino Villarreal was one of four military officers who was deployed by the federal government in May to stem a surge of violence in Tamaulipas.
The general was in charge of a northern zone that includes Nuevo Laredo, a city bordering Texas which has been the scene of turf wars between cartels fighting over control of the lucrative drug trafficking routes.
“The government of Tamaulipas condemns and deeply laments the death of General Ricardo Cesar Nino Villarreal and his wife,” the state’s security coordination group said in a statement.
Nuevo Leon’s chief prosecutor, Adrian de la Garza, had earlier said authorities were checking whether the general was one of the victims. Tamaulipas authorities said Nuevo Leon prosecutors had confirmed his identity.
De la Garza said the general usually travels in an armored vehicle with a security detail, but the victim was unarmed and in a civilian car.
Nino Villareal survived a previous attack on October 9 when unidentified gunmen shot at his armored vehicle in Linares, also in Nuevo Leon state.
Before his appointment in Tamaulipas, Nino Villareal was head of police in the Nuevo Leon town of Cadereyta.
The military took full control of security in Tamaulipas in May after scores of people died in a series of gunfights between warring cartels and clashes between gangs and security forces.
The state has been plagued by turf wars between the Zetas and Gulf drug cartels for years.
Both gangs have been weakened by the arrests or killings of top leaders.
The most recent violence has partly been blamed on infighting within the Gulf cartel.-AFP