A nonprofit group in contract with the city to provide shelter, examine and treat animals -- as well as dispose of their remains -- improperly stored its drugs, among other offenses, according to an audit released Sunday.

"It is inexcusable to have expired vaccines sitting in refrigerators that open and close next to employee lunches and the remains of dead animals," said New York City Comptroller Scott M. Stringer at an Upper West Side news conference, pointing to what he called a "system of dysfunction."

The audit by Stringer found Animal Care & Control of NYC, which has a five-year, $51.9 million contract with the city Department of Health, put animals' health at risk at shelters in Manhattan, Brooklyn and Staten Island. Auditors reviewed controlled substance logs kept between December 2013 and March 2014 and observed shelter conditions between March and November 2014.

Animal Care & Control, which takes in more than 30,000 animals annually, said in a statement it "has already undertaken steps to implement several of the recommendations in the Comptroller's report, and will continue to strengthen our policies and procedures."

Vaccines and employee lunches were found stored together at the Brooklyn shelter, and vaccines and animal remains next to each other at the Manhattan location. The logs showed nearly 500 times when expired drugs were given to animals. The organization additionally could not account for 239 tablets and the equivalent of 43 bottles of injectable liquids.

The report also found faulty ventilation resulting in a gas odor and a shared climate control system that increased the risk of spreading diseases between sick and healthy animals.

Stringer credited Animal Care & Control with appropriating $3.5 million for a new ventilation system and other work.

Deputy Comptroller for Audit Marjorie Landa said her agency received complaints of animals going in healthy and coming out sick, but the audit did not specifically track animals' well-being.

Stringer called for a computerized inventory system, the opening of more shelters, the creation of a fundraising component and more oversight that "the Department of Health has failed to provide."

The department in a statement said it is addressing concerns in the audit.