New York (CNN) -- Police will investigate the deaths of nearly 100 animals that were found in a Petco store after flooding in upstate New York, Johnson City Mayor Dennis Hannon said Monday.

Employees at the Oakdale Plaza store checked on the premises late Wednesday and "all was still well," Petco chief executive Jim Myers wrote Sunday on the chain's official blog, PetcoScoop.

"When the team members checked again early Thursday morning, the store was flooded with four feet of water and we were unable to enter," wrote Myers.

A river flood warning was issued Wednesday afternoon for the entire Johnson City area, along with flash flood warnings that continued well into Thursday, according to Joanne Labounty, a spokeswoman for the National Weather Service.

According to Hannon, a woman who identified herself as the manager of the store approached a firefighter who was near the Petco around 10:30 Thursday morning to request a boat. At that point, the store was under water, Hannon said, and there was not much the fire department could do.

Once employees were able to re-enter the store, they were able to rescue a majority of the animals, Myers wrote.

More than 100 small animals and three-quarters of the aquatic life were rescued, according to Lisa Epstein, a Petco spokeswoman. The small animals included an assortment of guinea pigs, mice, reptiles and birds.

Hannon questioned how the animals could have survived, recalling that "the floodwaters were very high, well above the front doors of the building. Unless the animals were very near the ceiling, a couple feet from it, they would have perished."

Hannon is upset that the store did not take more caution after he issued a state of emergency for Johnson City.

"The media was reporting that any area that was flooded in 2006 would be badly flooded again," Hannon told CNN, noting that the Oakdale Plaza was one of those areas.

The Johnson City store is a relatively new location, Myers wrote in his blog, and it was not in operation during the record high-river floods of 2006, and "we misjudged the risk to this location."

"We apologize to the members of the Johnson City community and look forward to serving you better in the future," Myers wrote.

Angry comments accompanied the blog post, with readers accusing the chain of making excuses. Several commenters said they had called PETA to report the incident.

"So many, so many residents are outraged over this, we owe it to the community to get to the bottom of it," Hannon said.

Epstein said Petco is internally investigating the incident as well.