Islip’s animal shelter director has retired amid preparations to fire her after she broke state law over a healthy puppy seized from his owner in a February drug raid, town officials said.

Joanne Daly, who became a lightning rod figure after several complaints, denied having the pit bull puppy, did not log him in and shuffled the dog “out the back door” to a rescue group, said James Heil, appointed late last year as commissioner of environmental control, which oversees the shelter.

In a recording that captured Daly’s side of a phone conversation three days after the Feb. 26 raid, she tells the caller, “I heard there was a raid in the evening. We got no call to come get a dog . . . I don’t have the pit puppy here.”

The dog’s owner, who was not arrested in the Central Islip raid, told Newsday she was on the other end of the call, and after the two hung up, Daly can be heard in the recording referring to a rescue group: “We’re going to have to lie. Bully Crew’s coming for the dog.”

The incident came on top of a January state inspection that found strays were transferred or adopted out before the mandated five-day hold, set in state agriculture law to allow owners to search for their missing pets.

“It was a violation of law,” Heil said about the puppy case. “There was no getting around it, no extenuating circumstances. The dog, when it was brought in, wasn’t registered, wasn’t tagged. It went out the back door to a rescue group.”

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Daly told town officials that she wanted to protect the puppy from going back to a known drug house, Heil said.

Daly, who had previously declined to comment, could not be reached Monday afternoon. Heil said her last day was Wednesday.

She started working there as a kennel aide about 16 years ago, then was chosen to head the shelter in 2007, although the countywide civil service list for shelter supervisor showed her at the bottom in test results.

Her departure had been awaited eagerly by several current and former workers.

Dogs languished at the shelter because Daly had a “chokehold” on adoptions, often rejecting potential adopters without taking applications and checking backgrounds, her critics said.

Adoptions rose in the time that Daly was off before her departure, one shelter employee said: “I believe last week we approved 10 adoptions, three of which were ‘long timers,’ in one day. That’s unheard of under Daly.”

But the pit bull puppy’s owner, Colleen Kester, 54, of Central Islip, fears she will never again see Chubbs, a Christmas gift. Bully Crew’s founder said the New Jersey family who adopted the dog won’t give him up.

Kester said she trusted the shelter when told Chubbs was not there, and she’s angry that Suffolk police and the town took her dog. Police also launched an inquiry.

“We laid together, we played together,” Kester said. “They had no . . . reason to steal my pup.”