Dogs are seen in cages on property belonging to puppy breeder Marilyn Shepherd last month in Ava, Mo. Missouri is the “puppy mill” capital of America, home to more than 4,000 shoddy dog-breeding businesses, according to one estimate. But now the chief of the state Agriculture Department is pledging to do more to crack down on bad breeders.

These puppies were among more than 100 injured and malnourished dogs rescued from a puppy mill in Winston, Mo., last week. Missouri is the “puppy mill” capital of America, home to more than 4,000 shoddy and inhumane dog-breeding businesses, by one estimate. But now the state is trying to clean up its reputation.

Seneca, Mo. ? When authorities raided J.B.’s Precious Puppies, they discovered more than 200 dogs standing in their own excrement, crammed three and four to a cage. Some were so sickly they were missing clumps of hair. The skeletal remains of puppies and adult dogs were found inside pet-food bags.

The ghastly scene deep in the Ozarks has become far too common in Missouri.

Missouri is the “puppy mill” capital of America, home to more than 4,000 shoddy and inhumane dog-breeding businesses, by one estimate. But now the state is trying to shed its reputation, with the chief of the Agriculture Department pledging to do more to crack down on bad breeders.

“Missouri led the nation in licensing breeders. Let’s lead the nation in putting unlicensed breeders out of business,” Agriculture Director Jon Hagler said.

Missouri has been No. 1 in puppy mills for decades, with fly-by-night breeders — both licensed and unlicensed — selling pups churned out by dogs that spend their entire lives in cages. The pets are sold through classified ads, in pet stores and over the Internet.

The problem is so severe that Missouri’s reputable breeders complain that the shady ones are making them all look bad.

Remote locations

Animal advocates say puppy mills flourish here for a number of reasons, among them: uneven enforcement of the rules, and remote, rural landscapes that allow poor or illegal practices to escape detection. The hills and hollows of the Ozarks have the state’s highest concentration of puppy breeders.

“It’s embarrassing,” said Julie Leicht, executive director of the Missouri Alliance for Animal Legislation. “We’re the meth capital. And we’re the leader in puppy mills. Welcome to Missouri.”

The stories are heartbreaking. In February, a raid in Missouri’s Pleasant Hope netted 93 Yorkshire terriers, their hair severely matted and covered in feces. Last September, 171 anemic, flea-infested cocker spaniels, some of them blind, were taken from a breeder. Fifteen days later, 67 emaciated, mangy dogs and puppies were rescued.

“Most people think puppies were born in a box next to a fireplace in somebody’s living room,” Kim Townsend, an activist who monitors the industry. “If they walked into these places, they’d be appalled.”

Improved enforcement

Since taking office in January, the agriculture chief has been working to better enforce a 1992 program for protecting animals cared for by breeders.

He has named a new program coordinator, asked for a re-examination of old cases, ordered a review of internal procedures, and stepped up inspections and the issuing of citations to violators. His new Operation Bark Alert allows people to report unlicensed breeders directly to him by e-mail.

But Hagler said his agency simply does not have the means to conduct inspections every year as required by law. “We cannot regulate 3,200 licensed breeders plus every animal rescue, shelter and dog pound, and go after unlicensed breeders with 11 total inspectors.”

The Humane Society of the United States’ “Stop Puppy Mills” campaign says Missouri should stop licensing breeders until it has enough inspectors.

State audits in 2001, 2004 and 2008 sharply criticized Missouri’s regulation of puppy breeders as ineffective and lax, citing management conflicts of interest, spotty inspections, few sanctions and failure to track repeat offenders.

State authorities can shut down breeders, revoke their licenses, fine them and ask local prosecutors to bring criminal charges of abuse or neglect. But Tim Rickey of the Humane Society of Missouri said the Agriculture Department rarely pursues charges.