The pilot of a suspected drug flight killed in an anti-narcotics operation in Honduras earlier this week was shot dead by two U.S. Drug Enforcement Administration agents after he refused to surrender, an agency spokeswoman said Sunday.

At the time, Honduran police said the twin-engine plane arriving from Colombia with a load of cocaine crashed while being chased by government aircraft. One pilot died in the July 3 incident and second was badly injured, but officials had not disclosed how the death took place.

DEA spokeswoman Dawn Dearden revealed on Sunday that when police arrived at the crash scene in eastern Honduras, they found the plane's two pilots. The injured pilot was arrested and the second was shot by the DEA agents after he ignored orders to surrender and made a threatening gesture, she maintained.

"Both suspects were given first aid and transported via helicopter to a secure location," Dearden said. "The pilot who resisted arrest died of his injuries."

She called the operation, which involved Honduran police and embedded DEA advisers, a success that resulted in the seizure of 900 kilograms of cocaine.

DEA agents embedded with police

It was the second time a DEA agent has killed someone in Central America since the agency began deploying specially trained agents several years ago to accompany local law enforcement personnel on all types of drug raids throughout the region.

U.S. officials say that in late June an agent shot a suspected drug trafficker as he reached for his gun in a holster during a raid in a remote northern part of Honduras. That operation resulted in the seizure of 360 kilograms of cocaine, the officials said.

Police ride on a truck with bags of some of the confiscated cocaine that was incinerated on the outskirts of Tegucigalpa on Wednesday. (Jorge Cabrera/Reuters)

A similar raid on May 11 killed four people, whom locals claimed were innocent civilians traveling a river in Honduras at night. Honduran police said the victims were in a boat that fired on authorities. The DEA said none of its agents fired their guns in that incident.

The deaths come amid an aggressive new enforcement strategy targeting countries like Honduras, which has become a major transshipment point for drugs heading to the United States. The country's remote Mosquitia region is dotted with clandestine airstrips and a vast network of rivers for carrying drugs to the coast.

The strategy involves a special team of DEA agents who work with Honduran police to move quickly and pursue suspicious flights, a U.S. official has said. Honduran and U.S. drug agents follow flights they detect of unknown origin and work with non-U.S. contract pilots.

While U.S. officials laud the strategy's successes in seizing cocaine and arresting traffickers, it has come under fire from human rights groups, especial after the May 11 killings.

International crackdowns in Mexico and the Caribbean have pushed drug trafficking to Central America, which is now the crossing point for 84 per cent of all U.S.-bound cocaine, according to Joint Task Force-Bravo, a U.S. military installation in Comayagua, Honduras.