Gov. Pat McCrory (R) said officials would work to quickly dispose of decaying animal carcasses that could contaminate waters and pose a potential public health threat. The state wants to avoid a repeat of the problems that followed Hurricane Floyd in 1999, when hundreds of bloated hog and chicken carcasses floated for days in floodwaters.

In his morning briefing, the governor said that “a lot of poultry and animals — a lot, thousands” already had drowned and that more casualties were still expected.

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“It certainly is a concern we have,” said Brian Long, a spokesman for the state Department of Agriculture and Consumer Services. “We do know of poultry farms being flooded, but we haven’t been able to confirm any hog losses…. Floodwaters are still cresting.”

Rick Dove, an environmentalist for the Waterkeeper Alliance, who landed from a surveillance flight late Tuesday afternoon, said the number of dead chickens “is probably in the millions.” He claimed to have seen thousands of floating carcasses.

“There’s a real problem here,” Dove said, estimating that “there could be tens of thousands of dead hogs.”

Matthew Starr, a riverkeeper who monitors environmental threats to the Upper Neuse River as part of the Waterkeeper Alliance, said photos show “floodwaters up to roofs of barns, mostly poultry…. I can’t confirm that there are animals in those facilities, but the flooding is quite terrible.” Asked about the scope of damage, Starr said, “The potential number? Oh God, that’s a number I can’t even make up. North Carolina is heavily inundated with swine.”

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Crystal Coast riverkeeper Larry Baldwin took part in a flight over several counties Tuesday morning. He said he saw some animal waste lagoons with water near them, including one facility in Duplin County that was completely surrounded by water. Most waste lagoons are in low-lying areas and near waterways, he said. “Some of these facilities are even surrounded on two or three sides by a creek.”

“It might not be as bad as Floyd,” Baldwin said. “It’s still bad.”

Eastern North Carolina is one of the top pork-producing regions in the state and home to the world’s largest pork production plant, which is located in the town of Tar Heel. More than 2 million hogs are raised just in Duplin County.

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The state doesn’t disclose the amount of waste the animals produce, but some organizations estimate it at more than 15 million pounds of manure annually. Another concern is hog and chicken waste washing into fresh water.

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“So far, we’ve not heard of any hog waste lagoons breaching as a result of the storm,” Long said. Were that to happen, the toxic waste would mix with sewer overflows contaminated with human waste from storm systems that couldn’t handle the hurricane’s deluge of rain.

The state Department of Environmental Quality said it was gearing up to dispose of thousands of carcasses. Secretary Donald R. van der Vaart said efforts will be made to place animals in lined landfills to protect groundwater from toxins leaching from their remains.

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Matthew threatened other animals, too. In Cumberland County, animal control workers raced to rescue hundreds of pets. John Lauby, director of the county’s animal control unit, risked his Chevrolet Tahoe SUV when he drove into Fayetteville’s badly flooded downtown on Saturday to save 30 dogs.

“I was driving that truck over water that reached the hood,” Lauby said. “It was that bad. Water was coming in filling the floor board.” All the dogs were saved and taken to a shelter, where they awaited their owners.

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“We’ve had tornadoes before, but this was just unreal stuff,” said Lauby, 73, a retired veterinarian. “I’ve been in monsoons in Vietnam and I’ve never seen 15 inches of rain in 24 hours like this.”

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Dead livestock wasn’t the only problem for farmers. Growers of soy, corn, peanuts and sweet potatoes that were still being harvested lost millions of dollars worth of crops when the wind and rains came.

It was the second consecutive year for crop farmers to be waylaid by fall rains. In October 2015, 10 straight days of rain ruined the harvest in eastern North Carolina.

“You’re talking about a back-to-back gut punch for these farmers,” Long said.

Ross reported from Raleigh, N.C., and Fears from Washington.

Correction: An earlier version of this post incorrectly named Robeson County.