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The year-old female was named Marama after being born last January to 6-year-old Gem.
The pair attracted such attention at the popular dog-walking beach that Department of Conservation staff placed protective fencing around them to ward off the possibility of dog attack.
Doc and Sea Lion Trust staff later moved the pair to the end of the peninsula, after deciding the risk of injury or harassment was too great, especially as Gem was preparing to leave the 5-day-old pup to feed at sea. Marama was found dead at Allans Beach on Saturday afternoon, Doc coastal ranger Jim Fyfe said yesterday.
''Marama had a good year.
''She was one of the largest and heaviest pups I've ever encountered.
''We sent the body to Massey University for autopsy and should have the results back in the next few weeks.''
New Zealand sea lions are listed as a critically endangered species and only returned to the Otago coast 19 years ago, after an absence of more than 200 years.
An average of four or five pups were born every year around Dunedin, Mr Fyfe said.
''Pups are usually born in late December and early January and we're expecting between six and 10 pups around the Otago coastline this year.
''People should expect to see wildlife in remote places this time of year.
''They can pop up in the weirdest of places and we want to know if people see any sea lions anywhere.''
A peninsula tour operator contacted the Otago Daily Times this week expressing concern at the number of dead red-billed gulls around the royal albatross colony at Taiaroa Head.
The ODT found 10 dead adults and three dead chicks in various stages of decomposition on Monday, but that was a natural attrition range in a colony of 4000 to 5000 birds, Mr Fyfe said.
''They're nationally classified as in decline, although that's not the situation in Otago.''
Anyone who locates a sea lion in residence is asked to contact Doc on 0800 DOCHOT (0800-362-468).firstname.lastname@example.org