The 52-year-old man allegedly made “threats to divulge untrue information about a police constable” in February, more than three months after the animal was found dead.
The defendant made a fleeting appearance at the Dunedin District Court where he had the matter administratively adjourned for three weeks.
He has interim name suppression until his next appearance.
The body of 11-month-old female sea lion Rua was found by Doc near Quarantine Point, north of the Portobello Marine Aquarium on November 6 last year.
A member of the public had reported seeing the lifeless animal to Doc.
Previous reports said Rua appeared to have been shot but according to court documents, the allegation is that the defendant stabbed the pup to death.
He faces a charge of taking a “Phocarctos Hookeri” - better known as a New Zealand Hooker sea lion – which has a maximum penalty of two years.
The man is also charged with wilfully ill-treating an animal causing it to die, under the Animal Welfare Act, and attempting to pervert the course of justice.
If found guilty of the latter, it may attract a potential jail term as long as seven years.
Doc Coastal Otago ranger Jim Fyfe said at the time the sea lion's death was "devastating''.
The New Zealand sea lion - population about 10,000 - is on the highly critical list.
Rua was just one of 11 sea lion pups born on the Otago Peninsula last year.
The arrest was the result of a joint investigation between Dunedin police, Doc and the Dunedin Sea Lion Trust, police said.
