Andres Lopez Elorez was arrested in Spain on a USA warrant and extradited to the United States on Monday.
It is believed the dogs were sent on flights to New York City, where the drugs were cut out and the animals likely died.
A vet has been accused of turning puppies into drug mules by stitching pouches of heroin inside their bellies. Prosecutors say between September 2004 and January 2005, Elorza was a member of a Colombian conspiracy that used pups and humans as couriers. Attorney's Office for the Eastern District of NY said. "Dogs are man's best friend and, as the defendant is about to learn, we are drug dealers' worst enemy".
A Colombian veterinarian is accused of implanting heroin in puppies to smuggle drugs into the United States. One Rottweiler was adopted by the Colombian National Police and later became a drug-detection dog, while a Bassett Hound puppy became a pet for another officer, the New York Times reported.
But Elorez evaded capture and spent the next decade on the lam.
His court-appointed lawyer told Magistrate Marilyn Go that Elorza had "certain psychiatric issues" as well as some kidney problems.
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A visibly upset Elorez gestured wildly with his hands to his interpreter. His attorney had no immediate comment. "I think a lot of this is stress-related", Mitchell Dinnerstein said.
He also has "a loving wife and two children" - and isn't actually a vet, the attorney later claimed.
Andres Lopez Elorza is pictured in this undated photo released by the Drug Enforcement Administration.
A status conference will be held on June 5, where both parties say they will explore a plea as a potential resolution.
U.S. officials say Elorez was part of a Colombian-based conspiracy from September 2004 to January 2005 that smuggled heroin into the United States using various methods to hide the narcotics from detection.