El Nino, the freak winds that have caused the worst weather in 40 years in many parts of the world, have also whipped up controversy within the Reagan administration.

The Agency for International Development has asked for $100 million for emergency aid to Peru, Ecuador and Bolivia, which have suffered $1.3 billion in damage from El Nino. But the Office of Management and Budget is "skeptical" of the proposal in a year of huge deficits, according to a spokesman.

The OMB spokesman suggested that Congress is already too far along in the 1983 appropriations process to consider the request for this year.

Twelve feet of rain has fallen in some parts of that region of South America, while drought has wiped out two-thirds of the crops in other areas, according to State Department officials. The infant mortality rate and the overall death rate have tripled, the officials said.

Tens of thousands are homeless as a result of the worst floods and droughts ever caused by El Nino, the Spanish words for "the child," so called because such weather phenomena normally come around Christmas.

But AID officials have said that the issue is political as well as humanitarian, because the disasters represent a danger to the elected governments of the three nations in question.

"The reaction of the people in those countries has been very emotional because they build and rebuild, and still the floods come again and wipe out what they have done . . . . They react with apathy and also with anger at the government," said Marshall Brown, AID deputy assistant administrator for Latin America.

An AID spokesman said the three Andean democracies "are under siege, not from Marxist guerrillas, but rather from the forces of nature which continue to punish the people and undercut support for the democratically elected governments."

An OMB spokesman said the debate over the emergency aid remains open. AID's Brown said that "the procedural objection is a bureaucratic one. It can be overcome if the will is there."

AID recently gave $52.6 million in Food for Peace aid to Peru, Bolivia and Ecuador, but agency officials said the disaster is of such magnitude that a significant portion of the entire economic output of those nations has been wiped out. Although it is now the dry season in Peru and Ecuador, El Nino rains continue at what a climate analyst at the National Oceanic and Atmospheric Administration called a "phenomenal" level.

In other areas, mainly in Bolivia and part of Peru, drought has wiped out two-thirds of the crops, according to AID officials who returned last week from the devastated region.

In Bolivia, 1.5 million people live in areas that have had no rain for eight months, and farmers have slaughtered so many of their animals that meat prices have dropped 75 percent. Vegetables are scarce and expensive; Bolivia this year has produced only about 300,000 tons of potatoes, the nation's staple crop, compared with the usual 900,000 tons, AID says.

Flooding in northern Peru has produced 60 to 70 percent unemployment. Piura, a city of half a million, has been completely cut off from land transport and must be supplied by air.

The country has lost 27 major bridges, and the Pan American Highway now ends in a lake several miles long in an area that used to be desert. About 40,000 adobe homes have melted in the flood, according to AID estimates, and another 40,000 have been damaged.

An AID spokesman said the situation is dangerous politically as well as economically. In Bolivia, "democratically elected President Hernan Siles Zuazo is trying to gain the . . . momentum necessary to avoid the fate of so many Bolivian presidents. In Ecuador, President Osvaldo Hurtado is trying to overcome the economic crisis through tough austerity policy measures . . . ."