Around 2,000 penguins have appeared dead on the coast of eastern Uruguay in the last 10 days, reports AFP.
However, the cause of this huge death, which does not appear to be avian influenza, remains a mystery, authorities said.
The Magellanic penguins, mostly juveniles, died in the Atlantic Ocean and were carried by currents to Uruguayan shores, said Carmen Leizagoyen, head of the Environment Ministry's department of fauna.
"This is mortality in the water. Ninety percent are young specimens that arrive without fat reserves and with empty stomachs," she said, and stressed that all samples taken have tested negative for avian influenza.
Magellanic penguins nest in southern Argentina. In the southern hemisphere winter, they migrate north in search of food and warmer waters, even reaching the coast of the Brazilian state of Espirito Santo.
"It is normal for some percentage to die, but not these numbers," Leizagoyen said, recalling that a similar die-off occurred last year in Brazil, for undetermined reasons.
Hector Caymaris, director of the Laguna de Rocha protected area, told AFP that he counted more than 500 dead penguins along six miles (10 kilometers) of Atlantic coast.
Environmental advocates attribute the increase in Magellanic penguin deaths to overfishing and illegal fishing.
"From the 1990s and 2000s we began to see animals with a lack of food. The resource is overexploited," Richard Tesore, of the NGO SOS Marine Wildlife Rescue, told AFP.
A subtropical cyclone in the Atlantic, which hit southeastern Brazil in mid-July, probably caused the weakest animals to die from the inclement weather, he added.
In addition to penguins, Tesore said he has recently found dead petrels, albatrosses, seagulls, sea turtles and sea lions on the beaches of Maldonado, a department east of the capital Montevideo.
Bd-pratidin English/Lutful Hoque