By Tom Knudson / The Sacramento Bee

The day began with a drive across the desert, checking the snares he had placed in the sagebrush to catch coyotes.

Gary Strader, an employee of the U.S. Department of Agriculture, stepped out of his truck near a ravine in Nevada and found something he hadn’t intended to kill.

There, strangled in a neck snare, was one of the most majestic birds in America, a federally protected golden eagle.

“I called my supervisor and said, ‘I just caught a golden eagle and it’s dead,’ ” said Strader. “He said, ‘Did anybody see it?’ I said, ‘Geez, I don’t think so.’

“He said, ‘If you think nobody saw it, go get a shovel and bury it and don’t say nothing to anybody.’ ”

“That bothered me,” said Strader, whose job was terminated in 2009. “It wasn’t right.”

Strader’s employer, a branch of the federal Department of Agriculture called Wildlife Services, has long specialized in killing animals that are deemed a threat to agriculture, the public and – more recently – the environment.

Since 2000, its employees have killed nearly a million coyotes, mostly in the West. They have destroyed millions of birds, from nonnative starlings to migratory shorebirds, along with a colorful menagerie of more than 300 other species, including black bears, beavers, porcupines, river otters, mountain lions and wolves.

And in most cases, they have officially revealed little or no detail about where the creatures were killed, or why. But a Bee investigation has found the agency’s practices to be indiscriminate, at odds with science, inhumane and sometimes illegal.

The Bee’s findings include:

• With steel traps, wire snares and poison, agency employees have accidentally killed more than 50,000 animals since 2000 that were not problems, including federally protected golden and bald eagles; more than 1,100 dogs, including family pets; and several species considered rare or imperiled by wildlife biologists.

• Since 1987, at least 18 employees and several members of the public have been exposed to cyanide when they triggered spring-loaded cartridges laced with poison meant to kill coyotes. They survived – but 10 people have died and many others have been injured in crashes during agency aerial gunning operations over the same time period.

• A growing body of science has found the agency’s war against predators, waged to protect livestock and big game, is altering ecosystems in ways that diminish biodiversity, degrade habitat and invite disease.

Sometimes wild animals must be destroyed – from bears that ransack mountain cabins to geese swirling over an airport runway. But because lethal control stirs strong emotions, Wildlife Services prefers to operate in the shadows.

“We pride ourselves on our ability to go in and get the job done quietly without many people knowing about it,” said Dennis Orthmeyer, acting state director of Wildlife Services in California.

Basic facts are tightly guarded. “This information is Not intended for indiscriminate distribution!!!” wrote one Wildlife Services manager in an email to a municipal worker in Elk Grove about the number of beavers killed there.

And while even the military allows the media into the field, Wildlife Services does not. “If we accommodated your request, we would have to accommodate all requests,” wrote Mark Jensen, director of Wildlife Services in Nevada, turning down a request by The Bee to observe its hunters and trappers in action.

“The public has every right to scrutinize what’s going on,” said Carter Niemeyer, a former Wildlife Services district manager who worked for the agency for 26 years and now believes much of the bloodletting is excessive, scientifically unsound and a waste of tax dollars.

“If you read the brochures, go on their website, they play down the lethal control, which they are heavily involved in, and show you this benign side,” Niemeyer said. “It’s smoke and mirrors. It’s a killing business. And it ain’t pretty.

“If the public knows this and they don’t care, I’m not going to lose any sleep over it,” Niemeyer said. “But they are entitled to know.”

Agency officials say the criticism is misleading. “If we can use nonlethal control first, we usually do it,” said William Clay, deputy administrator of Wildlife Services. “The problem is, generally when we get a call, it’s because farmers and ranchers are having livestock killed immediately. They are being killed daily. Our first response is to try to stop the killing and then implement nonlethal methods.”

In March, two congressmen – Reps. John Campbell, R-Irvine, and Peter DeFazio, D-Ore. – introduced a bill that would ban one of Wildlife Services’ most controversial killing tools: spring-loaded sodium cyanide cartridges that have killed tens of thousands of animals in recent years, along with Compound 1080 (thallium sulfate), a less-commonly used poison.

“This is an ineffective, wasteful program that is largely unaccountable, lacks transparency and continues to rely on cruel and indiscriminate methods,” said Camilla Fox, executive director of Project Coyote, a Bay Area nonprofit.

“If people knew how many animals are being killed at taxpayer expense – often on public lands – they would be shocked and horrified,” Fox said.