Peru's northern beaches have been declared off-limits as scientists scramble to pin down the cause.
Since March some 4,000 birds, mostly pelicans and boobies, have been found dead.
Since January 900 dolphins carcasses have littered the beaches.
Many speculations on the cause have been made, but nothing has been linked for certain.
The deputy minister of fishing is resigning because the sector is "in disorder, full of irregularities, and corruption."
Peru's northern beaches have been declared off-limits as scientists scramble to pin down what is causing the mysterious deaths of thousands of birds and dolphins.
Since March some 4,000 birds, mostly pelicans and boobies, have been found dead along a 200-kilometer (120 mile) stretch of northern coastline reaching up to the border with Ecuador along with at least 900 dolphins.
The South American nation's health ministry declared an alert at the weekend, urging the public to stay away from the beaches around Lima and on the northern coast until the cause of death is known.
For the time being, the state environment ministry has ruled out water contamination or damage from dragnet fishing, suggesting cautiously that wildlife may be falling victim to a virus.
"Once we know what the scientific causes behind these deaths are, we will lift the alert," said health ministry spokesman Bernardo Ausejo, adding the investigations could take another five to 10 days.
A team of ornithologists have also been investigating the mysterious death of the birds which started after dead dolphins began to wash ashore in January in the northern departments of Piura and Lambayeque.
But biologist Guillermo Boigorrea, from the agriculture ministry in Lambayeque, said although nothing had been determined for sure, "it seems that the birds died of starvation.
"Now we have to find out why the birds can't fly or fish," he said, adding scientists had also been analyzing the seawater.
"It's unbelievable that the Oceanic Institute has still not given a reason for the massive deaths of pelicans and dolphins," said Carlos Bocanegra, a renowned biologist from the University of Trujillo.
"I believe we are trying to protect certain interests," he told Peruvian radio, in an allusion to the powerful fishing industry, which is one of the mainstays of the nation's economy.
One non-government conservation organization, known as ORCA, has blamed the dolphin deaths on oil exploration activities in the area, which it claims produces noises which are having an acoustic impact on the mammals.
The huge die-off "is a risk for human health in case of a possible mutation of the virus," said German biologist Stefan Austermuehle, head of another environmental group Mundo Azul. Local health officials are also asking residents not to eat raw fish, to avoid swimming in the seas and to stay away from beaches where animals have been found dead. On Tuesday red flags were flying on some of the beaches warning of the danger.
Former health minister Uriel Garcia blamed excessive fishing for the pelican deaths, saying stocks of some species were running low such as anchovies, a favorite food of the sea-birds.
In an editorial with the daily El Comercio, he also maintained the birds were dying of starvation, not sickness.
And weather expert Abraham Levy hypothesized that the warming of the Pacific waters due to El Nino could be to blame. (Though the Pacific was experiencing a La Nina until recently.)
"The warming of the waters alters the food chain, which is very complex and starts with the plankton and ends with the marine birds and the marine mammals on the other," he told AFP.
Meanwhile, deputy minister of fishing Patricia Majluf said she was resigning on Friday as the sector was "in disorder, full of irregularities and corruption."