At a remote research center on the Nebraska plains, scientists are using surgery and breeding techniques to re-engineer the farm animal to fit the needs of the 21st-century meat industry. The potential benefits are huge: animals that produce more offspring, yield more meat and cost less to raise.

There are, however, some complications.

Pigs are having many more piglets — up to 14, instead of the usual eight — but hundreds of those newborns, too frail or crowded to move, are being crushed each year when their mothers roll over. Cows, which normally bear one calf at a time, have been retooled to have twins and triplets, which often emerge weakened or deformed, dying in such numbers that even meat producers have been repulsed.

Then there are the lambs. In an effort to develop “easy care” sheep that can survive without costly shelters or shepherds, ewes are giving birth, unaided, in open fields where newborns are killed by predators, harsh weather and starvation.

Last Mother’s Day, at the height of the birthing season, two veterinarians struggled to sort through the weekend’s toll: 25 rag-doll bodies. Five, abandoned by overtaxed mothers, had empty stomachs. Six had signs of pneumonia. Five had been savaged by coyotes.

“It’s horrible,” one veterinarian said, tossing the remains into a barrel to be dumped in a vast excavation called the dead pit.

These experiments are not the work of a meat processor or rogue operation. They are conducted by a taxpayer-financed federal institution called the U.S. Meat Animal Research Center, a complex of laboratories and pastures that sprawls over 55 square miles in Clay Center, Neb. Little known outside the world of big agriculture, the center has one overarching mission: helping producers of beef, pork and lamb turn a higher profit as diets shift toward poultry, fish and produce.

Since Congress founded it 50 years ago to consolidate the United States Department of Agriculture’s research on farm animals, the center has worked to make lamb chops bigger, pork loins less fatty, steaks easier to chew. It has fought the spread of disease, fostered food safety and helped American ranchers compete in a global marketplace.

But an investigation by The New York Times shows that these endeavors have come at a steep cost to the center’s animals, which have been subjected to illness, pain and premature death, over many years. The research to increase pig litters began in 1986; the twin calves have been dying at high rates since 1984, and the easy care lambs for 10 years.

As the decades have passed, the center has bucked another powerful trend: a gathering public concern for the well-being of animals that has penetrated even the meat industry, which is starting to embrace the demand for humanely raised products.