The world's largest ocean is hosting the yin and yang of El Nino.

On one side of the Pacific, large tracts of Australia are gripped by drought triggered by the phenomenon. On the opposite side, the desert coastline of Peru is preparing for devastating rain.

Scientists warn Peru faces one of the strongest El Ninos on record.

In the next few months it could deliver a multi-billion-dollar damages bill from landslides, floods, failed crops and the collapse of the world's largest anchovy fishery.

"Peru, along with Australia, is one of the worst affected countries in the world from El Nino," said Angel Cornejo, professor of climate studies at the National University Agraria in the Peruvian capital, Lima.

"Poverty is the problem here. People live in places that will flood. They are very poor and they have nowhere else to go."

The government declared emergencies in 14 districts, including Lima, and funded preparation efforts.

The last severe El Nino, in 1998, had a calamitous impact causing floods in the Andes and on the coast, destroying more than 12,000 homes, damaging half the country's transport infrastructure and leaving a $A4.9 billion repair bill.

In Peru's second largest city of Trujillo, residents are bracing for torrential rain which may begin later this month.

The desert city and its population of 1 million people usually receive less than 50 millimetres of rain a year.

Part of the roof of Doralisa Cruz's mud brick home is missing and she fears her house in Trujillo will flood as it did during the last severe El Niño ( ABC News: Krista Eleftheriou )

During the last major El Nino, 3,000 mm of rain fell between November and March.

"My house was like a lagoon. Water covered half of my body," Doralisa Cruz, 70, said.

"There was a fast-flowing river [which appeared nearby] and lasted two months. Only two houses resisted the flood. The others disappeared."

Ms Cruz lives in El Porvenir, a suburb of Trujillo, where more than half the population is below the poverty line.

During 1998, rivers carved their way through Trujillo and its cemetery, carrying bodies into the colonial town square.

Since then, internal migrants from Peru's mountain region have moved to the city and some have built homes in the dry river beds.

"If El Nino hits, our major fear is that three dry river channels will start to flow," Olga Castro, head of risk and disaster Management at the city's Civil Defence Service, said.

"We went to the places where the channels were and we found that people have bought pieces of land and they have built houses. We told them to leave but they do not want to."

Ms Castro warned if there were floods, diseases such as dengue fever and cholera would be major problems.

She said the Civil Defence Service was encouraging people to prepare their homes and clean their roofs to prevent them collapsing, but few people have money for protection works.

Peruvian fishermen bear the brunt of climatic event

Huanchaco fisherman Victor Arzola uses his traditional caballito de totora boat to fish. His daily catch has dropped from 80kg to just a small bag due to El Niño. ( ABC News: Krista Eleftheriou )

During El Nino, the warm water from Indonesia moves east and the prevailing winds reverse, travelling from west to east, generating heavy rainfall in parts of South America, and in particular Peru's northern coast.

Peruvian fisherman were the first to name the climatic event, calling it El Nino de Navidad or Christmas Child.

In Trujillo's beachside suburbs, it is the fishermen who are experiencing the initial impact of the latest El Nino as the ocean becomes warmer.

"We normally have 80 kilos of fish a day, now it's just enough for personal food," Victor Arzola, vice-president of the Traditional Fishermen's Association in Huanchaco, said.

Here, fishermen use traditional caballito de totora boats made from reeds.

"During the last big El Nino we stopped fishing and worked as builders," Mr Arzola said.

Peru has the world's largest stock of anchovy, but fisheries professor Luis Icochea from the National University Agraria said this year's catch had more than halved to 2.5 million tonnes and was expected to decline further over the next six months.

"The anchovies have travelled south and dived deeper where the fishermen's nets cannot reach, because they don't like the warm water," Professor Icochea said.

"Next year will not be good because the anchovies will have problems reproducing."

El Nino fund established to protect archaeological sites

Roof structures protect the UNESCO listed ancient ruins of Chan Chan in northern Peru. ( ABC News: Krista Eleftheriou )

Meanwhile, in an unprecedented move, the Peruvian government has established a $A3.94 million fund for El Nino protection works at archaeological sites, including South America's largest pre-Columbian city of Chan Chan.

The site marked the rise of the Chimu people who dominated the region between the eighth and 15th centuries.

The UNESCO-protected structures in the 14 square kilometre beachside desert ruin are made of sand and mud bricks and are particularly susceptible to rain erosion.

Protection works have become all the more important after the discovery in recent weeks of a new temple containing 31 skeletons, the first such find in 40 years.

"This is one of the most important discoveries. There is a central body surrounded by other people," Cezar Mora, archaeologist and assistant director at Peru's Ministry of Culture, said.

A similar discovery of a temple containing 300 skeletons in the 1970s revealed it was a Chimu King surrounded by wives, daughters or female servants who either voluntarily or forcibly joined their king shortly after his death.