New York City is once again looking for someone to head up the city’s animal shelters.

For the third time in six years, the struggling nonprofit group that handles animal control for the city is looking for a new leader.

The search comes as the city Health Department is negotiating a new multi-year contract with New York City Animal Care and Control to continue to run its shelter system.

Activists are seizing the moment, saying it’s a rare chance to focus attention on chronic problems at the shelters.

Queens and the Bronx are still without shelters, despite a city law signed in 2000 mandating them. Old facilities with poor ventilation means more animals get sick, advocates said. And rescuers are taking fewer pets from AC&C because sicker animals mean higher veterinary bills.

As a result, thousands of dogs and cats are euthanized due to illness, behavioral problems, lack of space and the grim fact that no one steps forward to adopt them, advocates said.

“The city has never given [AC&C] the money it needs,” said Esther Koslow, a former volunteer who started a petition drive to get the attention of Health Commissioner Thomas Farley.

“You need shelters that don’t make the animals sick,” Koslow said, adding that AC&C staff “are too quick to deem stressed-out, caged animals as unadoptable.”

But the group won’t be getting any more money from the city. In fact, Farley recently said the annual budget – which has hovered at around $8 million to $9 million in recent years – will be slashed again next year.

“We need a shelter professional who is committed to the idea of managing that place to excellence,” said Jane Hoffman of the Mayor’s Alliance for NYC’s Animals, a nonprofit group that provides grants to rescuers who pull animals from AC&C shelters.

“I know they have some good candidates. I hope they get it right,” she said.