Police said Colonel Porfirio Cedeno, who led an air force special operations unit, was shot multiple times in the city of Guayaquil while traveling to a military ceremony.
More than 20 shots were fired at the pickup truck transporting him, and the driver was hit in the leg, said police official Santiago Tuston.
Cedeno was traveling from Guayaquil to Manta about three hours away. Both cities have been caught up in fighting between rival drug gangs that has seen homicide rates in Ecuador soar.
The truck ended up stalled in the middle of the road with shattered windows, its body riddled with bullet holes, AFP observed.
Police recovered more than 20 casings at the scene. Investigators believe the gunmen were also traveling by car.
Cedeno had headed a special unit focused on combatting drug trafficking, contract killings and extortion in the city of Duran neighboring Guayaquil.
Defense Minister Gian Carlo Loffredo said the colonel's murder should be answered with "a war cry" against organized crime.
"It is in our hands to turn this act of cowardice into the end of an era of terror and of the miserable people who led it," he said.
The military issued a reward -- the amount was not specified -- for the arrest of those responsible for the killing.
- 'Dear friend' -
Ecuador is home to an estimated 20 criminal gangs involved in trafficking, kidnapping and extortion, sowing terror in the country of 18 million squeezed between the world's biggest cocaine producers, Peru and Colombia.
In recent years, the nation has been plunged into violence by the rapid spread of transnational cartels that use its ports to ship drugs to the United States and Europe.
In 2023, Ecuador registered a record 47 homicides per 100,000 inhabitants.
Under a state of emergency and military crackdown launched by President Daniel Noboa, in office since November 2023, that figure dropped to 38 per 100,000 last year, according to official data.
Noboa is seeking a new term in elections that will go to a runoff in April after an inconclusive first round last Sunday saw him narrowly pip challenger Luisa Gonzalez.
In a message on social network X, ex-president Rafael Correa paid homage to his "dear friend" Cedeno, who had served as a member of his security team.
And the presidency in a statement said the events "demonstrate the state of war in which Ecuador is immersed."
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