OLIVETTE — The state of Missouri has rejected St. Louis County’s application for an animal shelter license, required by law to operate, after the county shelter failed three state inspections since February.

The state cited violations for holding dogs in cages too small for them, failing to clean up feces in play yards, and allowing bugs in food storage areas, among other problems.

“They are not operating under a license and we would very much like for them to get under a license,” said Christi Miller, a spokesperson for the Missouri Department of Agriculture.

Miller said the county is “working hard to get into compliance to receive a license.” But the state wants the county to get one as soon as possible. “The rules are the rules and the law is the law,” Miller said.

St. Louis County spokesman Doug Moore said the animal shelter submitted another application Friday under its new director, Malik Johnson.

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The state rejection comes after years of tumult, then big changes at the animal shelter.

The nonprofit Animal Protective Association, which also runs its own shelter in Brentwood, left the shelter in February after running it for two years. The county contracted with the APA following various problems under county management, including euthanasia scandals , overpopulation, poor conditions and other problems.

The APA was lauded for cleaning up the facility and boosting adoptions. In August, the nonprofit said it accomplished its mission and would withdraw from the county contract, three years before it was set to expire. Records later showed its departure also stemmed from the county rejecting APA invoices for items such as meals, team outings and dog training.

But there were worries soon after. In April, the county announced a dangerous parvovirus outbreak.

On May 2, the county health department said in a news release that it had euthanized 19 dogs that had shown symptoms and tested positive for the virus. On May 9, the shelter’s medical director quit .

Meanwhile, the county was trying to obtain its state license.

When St. Louis County took over shelter operations from the APA, it had to obtain a new license from the agriculture department, according to Miller, the department spokesperson. To get a new license, the shelter needed to score perfectly on state inspections, with no violations.

A state inspector, Olivia Bennett, first visited the shelter on Feb. 13, about a week before the APA handed operations back to the county. The inspection applied to both the APA and the county. Bennett found seven violations, according to her report.

Pull cables on doggy doors to kennels had fallen off the track or were damaged. A large pipe in one of the shelter’s enclosures was rusted, and dog hair had accumulated on top of the enclosures. Two dogs, Gingerbread and Nugget, were in kennels that were too small for them. Roaches and gnats were in the food storage area. The shelter had expired medications on hand, and a few kennels had unconsumed medication on the floor.

The county had 90 days, including two more inspections, to bring the shelter into full compliance.

Bennett came back in March, and found improvements: The pull cables were fixed. The rusted pipe had been painted. The dog hair was removed. All dogs were in appropriately sized cages. There were fewer bugs and no expired or unconsumed medications.

But there were new problems. A few large drains in between rooms were clogged up, causing at least an inch of standing water to gather in front of animal enclosures. Bennett also found feces in “numerous outdoor play yards” that hadn’t been totally cleaned up. Those areas must be sanitized in between different animals using them.

The state said it would come back on May 14.

When Bennett returned, she found the drainage issue between rooms had been fixed. The play yards were clean, although not in use.

But she found seven new violations: Several dogs had puddles of water in their enclosures. At least four dogs were in cages that were too small for them. Several dogs were in “freestanding wire cages” that didn’t have enough head space for them to stand normally. Two dogs were in cages without identification cards. Swarms of gnats were in various rooms. Supplies of dog food were left open, and expired medications were present.

“The applicant has failed to meet total compliance in three inspections over 90 days,” Bennett’s report stated.

The state denied the county’s application for a license.

Operating an animal shelter without a license is a class A misdemeanor, according to state law. Class A is the most serious class of misdemeanors, punishable by up to a year imprisonment and a fine of up to $2,000, or both.

After failing an initial application, an applicant “may reapply after six months from the date of the last failed inspection,” according to state law.

The state won’t make the county wait that long, nor will it pursue any charges or shut the shelter down, said Miller, the state spokesperson. “We certainly don’t want it to come to that,” she said.

Moore said the animal shelter needs to reduce its population before it can pass an inspection.

Shelter leaders want to do that by waiving adoption fees, boosting its foster program and expanding efforts to reunite stray pets with their families.

The county will ask the state to come back once the shelter is “comfortably hitting our capacity levels,” Moore said.

The shelter plans to host an adoption event almost all day Saturday.