Enforcement officers from Staffordshire County Council visited Swan Pit Crematorium after complaints that customers had paid to have their pets cremated but had not received the ashes.
The authority has confirmed it has launched a probe into the business in Gnosall.
Cat lover Cynthia Keaton Tennant says she was contacted by a senior enforcement officer who told her they had discovered the body of her pet Boy George being stored at the premises.
The 60 year old retired minister says she was tracked down by the micro chip inside her cat.
"I just kept asking the officer to explain, I couldn't understand," she said. "I had his ashes on my bookshelf, yet this woman was telling me he had never been cremated."
Miss Tennant from Hopton Court in Stafford, claims officers took away the casket with what she believed held Boy George's remains it was confirmed it was not cat DNA but horse ash.
The caskets of Miss Tennant's four other cats will be examined and used as evidence.
Officers originally began their investigations after a complaint dating back to 2010.
County Councillor Gill Heath, cabinet support member for Environment and Rural Issues, said: "We have received complaints about Swan Pit Pet Crematorium in Gnosall, and are currently investigating their operating practices.
"Animal Health in this instance acted on a tip-off from a member of the public. When this happens, they launch an investigation and if needed, will execute a warrant on an identified premises along with police.
"If issues are identified at the premises, the investigation will continue and witness evidence will be gathered. If this is substantial they will look to take those being investigated to court."
Anyone who has used the crematorium in the last few months is asked to contact Staffordshire County Council's Animal Health team on 01785 277875.
Allan McMasters, owner of Swan Pit Crematorium, declined to comment.