The daily extinction of plant and animal species may prove to be the worst and costliest desecration that mankind has yet visited upon the planet, the Council on Environmental Quality reported yesterday.

Shifting the major focus of its annual report from domestic to an international environmental concern for the first time, CEQ warned that deforestation and the spread of deserts are wiping out as many as three species of life every day right now. "A rate of one per hour is likely by the late 1980's," CEQ Chairman Gus Speth told an earlier news conference. t

Domestically, however, U.S. environmental programs "are producing tangible benefits," President Carter said in transmitting CEQ's 11th annual report to Congress. "By and large, water quality in our rivers and lakes has stopped deteriorating. Levels of certain damaging pesticides in the environment have ceased to climb . . . .

The signs are unmistakable that we in the United States are learning how to live in balance with nature," Carter's statement said.

Continuing and growing problems include chemical pollution of groundwater, which is the drinking water supply for half the country, and the spread of deserts in the West. Issuing separate lengthy reports on both matters, CEQ said deserts now are "severe" in a western area the size of the original 13 colonies.

Caused in low-rainfall areas by overgrazing, overcutting of trees, urban sprawl, faulty drainage and reckless use of groundwater, the result is a denuded landscape of eroded gullies, salty soil and blowing dust. In 1977, the report notes, a windstorm moved 25 millions tons of soil out of one 373-acre piece of the San Joaquin Valley in California within 24 hours.

Council member Jane Yarn said the best hope lies in "nontechnical, nonstructural" solutions like water and soil conservation "that benefit the general public but not necessarily any single interest."

Similarly, council member Robert Harris said that chemicals from decades of careless waste disposal have begun to cause "serious" groundwater contamination in at least 34 states. "Groundwater aquifers are like dark refrigerators" that preserve the chemicals in a cold, airless environment that is nearly impossible to clean, he said. "None of the compounds so far reported has a beneficial role in human or animal health," they study said.

The Chemical Manufacturers Association issued a reply criticizing the groundwater report for focusing "a disproportionate amount of attention" on chemicals when, according to the association, a 1977 report to Congress found faulty septic tanks to be the major groundwater polluter.

The CEQ annual report cited three "new stresses" sure to complicate efforts to deal with water loss and pollution in the West: rising agricultural prices that encourage farmers to grow more crops; the energy crunch that means water-costly development of massive coal and oil shale deposits, and the projected siting of the MX missile, which will draw hundreds of thousands of people and massive construction to a delicate, arid area.

Species loss increases in polluted areas or places turning to deserts, the report said.As many as 20 percent of the world's 5 million to 10 million existing species could be lost by the turn of the century, most of them in tropical areas now being slashed and burned, and nearly all will vanish without ever having been evaluated for possible benefit to humankind.