Animals are being accidentally euthanized and getting poor medical treatment at city-controlled shelters, a former Animal Care and Control vet charges in a new lawsuit.

Dr. Njeri Cruse claims dogs and cats suffered during her two-year stint as ACC’s medical director because she was repeatedly undermined by a pencil-pushing administrator who ignored her medical advice.

She alleges that ACC Executive Director Charlene Pedrolie, who left the agency in 2009, “would often dismiss or override medical decisions, which I made, without sufficient knowledge and with no sound justification.”

Pedrolie ignored complaints about a Manhattan shelter staffer who repeatedly made mistakes about “euthanasia decisions,” the suit claims.

When the staffer sent a pooch that should have been reunited with its worried owner to the death chamber, Cruse complained, but Pedrolie allegedly told her to mind her own business.

Cruse said she was forced to resign in 2007, after nine years at ACC, because she was being undermined.

Cruse, who is seeking unspecified damages for her forced departure, declined to comment on the court papers.

Animal Care and Control declined to comment on the pending litigation.