SAN RAFAEL, Calif. -- A North Bay animal shelter has been shut down following a surprise inspection.

The Marin Humane Society said it found cats and dogs at the Milo Foundation Shelter in San Rafael living in filthy and overcrowded conditions.

Complaints of mismanagement led officials to the Milo Foundation Shelter on Fourth Street.

Once inside, they said they didn't like what they saw. They pointed to dirty conditions, crowded kennels and illegal medications.

Some of the animals were taken to the Marine Humane Society in Novato.

One was a little chihuahua mix that the Humane Society said was barely breathing and had fresh wounds from a dog attack.

"Those injuries resulted in her lung being penetrating and why she was coughing and wheezing," said Captain Cindy Machado of the Marin Humane Society.

Machado also said nine cats suffering from ringworm and other infections were seized. "A couple have ear mites. And this guy has a lesion on his leg; that mean's very contagious," said Machado.

Officials with the Marin Humane Society say Thursday morning's surprise inspection uncovered several health and safety violations.

"What we found were layers and layers of greasy grime, fur and feces caked on cage wiring, in the drain, on the floor, on the walls," explained Machado. "Granted, in their minds we caught them on a bad day. In our mind, it was months and weeks of improper cleaning protocols."

Milo Executive Director Lynne Tingle denied the allegations. She said the early morning inspection didn't allow her staff time to clean up. "There is no facility -- I don't care what kind of facility that has cats, kittens, dogs and puppies -- that is clean and smelling like daisy at 7 in the morning," said Tingle.

Tingle admitted having more animals than permitted by the city, but said she was in the process of requesting the permit be changed to allow more dogs on site.

She said the raid is part of a vendetta by a disgruntled employee and added the foundation has rescued thousand of animals during the last 15 years. "Every animal that's here would have been dead. We rescue them from kill facilities," said Tingle.

Clemente Pryor said she first stopped by the shelter in August and came by Monday to provide a foster home for a cat. "I know they are a really good organization and they are really well known in the community. I hope that things work out," said Pryor.

The Milo staff has spent the past couple of days cleaning, but the Humane Society said it's not enough. Officials said they want to see major changes and will work with the Foundation to develop a plan to address the issues.