In a quiet, rural tract of southern Florida, where income from the land far surpasses that from tourists’ pockets, one industry has gone almost unnoticed despite raking in some big dollars over the last 15 years.

But now, just like a noisy squabble among an excitable troop of monkeys, there is suddenly trouble in a once-happy camp. In a scandal that has become known locally as Monkeygate, federal and district authorities are looking into the monkey breeding farms of Hendry County. They don’t like what they see.

Until now, monkey farming has been a lucrative yet low-key business in a region better known for its plentiful citrus groves. County officials welcomed with open arms the companies that breed and sell the long-tailed macaques for research. With three large farms in operation and approval pending for a fourth, Hendry is a world leader in the specialist trade.

But the recent emergence of an undercover video shot by animal rights activists at one of the farms – which purported to show workers physically abusing monkeys and other primates with injuries including exposed tailbones – is only the latest in a series of developments since late last year that have threatened that expansion.

The video, filmed by an activist for the People for the Ethical Treatment of Animals (Peta), prompted an inspection last month of one farm, Primate Products Inc, by the US Department of Agriculture (USDA). A damning report highlighted the “trauma, pain, injuries and stress” suffered by the monkeys.

That followed a lawsuit against Hendry by the Animal Legal Defense Fund, which alleges that facilities were approved without the required public hearings; an ongoing inquiry by the county into alleged code violations by the companies, including that they conducted prohibited experiments on the monkeys; and a growing public backlash as previously unaware residents learned the scale of the industry on their doorstep.

“There are people two miles from the farms that had no idea what was going on there,” said Madeleine Doran, one of the leaders of an increasingly vocal opposition movement whose members have staged several protests and harnessed social media to get their message out.

“Now, with the lawsuits and the inspections, everyone is aware of it. We want an immediate halt to importing of monkeys to Hendry County and ultimately we would like to see all of the facilities shut down.”

Doran believes the inquiry launched by Hendry County is merely “a smokescreen” to give the impression that it is taking complaints seriously.

“What’s disturbing is the secrecy surrounding all of it,” she said. “The county have stonewalled us and won’t answer any questions about it.”

In a statement to the Guardian, a Hendry County spokeswoman confirmed it was looking into alleged land-use violations and that it was waiting for documents requested from the Florida fish and wildlife conservation committee and the USDA.

“We do not currently have any indication of a timeframe for the requested documents. Once Hendry County is in receipt of said documents a full review will be done and a determination will be issued,” the statement said.

Asked if the inquiry meant that Hendry was not as welcoming to the industry as it once was, the spokeswoman said: “Hendry County has been consistent in our message: we stand behind the rights of our property owners afforded to them by right.”

To Doran, the thousands who have signed a petition protesting the industry’s expansion, and the animal rights groups also fighting for an end to what they see as a barbaric trade, the county is dragging its heels.

Justin Goodman, director of Peta’s laboratory investigations department, pointed out that USDA inspectors moved in quickly to demand action by Primate Products to correct violations of the animal welfare act. One particularly harrowing scene in the group’s video shows a worker holding a monkey upside down by its tail as he uses a finger to shove the animal’s prolapsed rectum back in, while other shots show employees forcefully pulling monkeys from fences by their tails and other primates cowering in the corner of filthy cages.

“Hendry citizens and leadership are being exploited by companies bringing a cruel trade and health risks to their area,” Goodman said. “These companies prey on communities in need of an increasing tax base, or ones that are quite rural and don’t know what they’re getting themselves into.

“Here we have the greatest concentration of monkey farms in the world. They have no place in Hendry County and no place in the 21st century, and we want to see them all shut down.”

A lawsuit against the county is ongoing. In November, the California-based Animal Legal Defense Fund (ALDF) filed a complaint in Florida’s circuit court claiming that Hendry approved a primate breeding facility operated by a company called SoFlo Ag at a closed-door meeting, in contravention of the state’s so-called sunshine law.

In May the group amended the suit to add the name of the Mauritius-registered company Bioculture, which it alleged was also the beneficiary of secret approval to expand on to land owned by a company called Panther Tracts that already houses Primate Products and more than 3,000 monkeys.

The ALDF, which wants both permits revoked, says the farms pose a significant health risk to the local community because monkeys can carry the Ebola virus, tuberculosis and herpes B.

“Escaped exotic monkeys and the waste produced by thousands more animals on the Panther Tracts property could also damage the fragile ecosystem of the Big Cypress National Preserve, which is already struggling with an invasion of non-native Burmese pythons,” said ALDF spokeswoman Megan Backus.

Peta’s video investigation of Primate Products in Hendry County, Florida. Some viewers may find this content disturbing.

Jeff Rowell, the president of Primate Products, said he expected a fine following the USDA inspection and that his company was taking measures to fix the violations.

“I can’t just sit on my hands,” he said in an interview with the News-Press. “I’m accountable to clients, I’m accountable to the county and I’m accountable to the public.

“The biggest consequence is losing public trust. This is much harder to recover, but we are determined to try.”

Rowell admitted he was “shocked” by the treatment of some of the monkeys in the Peta video but claimed some of the other scenes were unfair.

“They film at 7.30 in the morning, then they claim the animals are living in filthy conditions,” he said. “Of course the cage looks its worst at 7.30 in the morning. Trust me, those cages are cleaned every day. It’s all about the context.”

To Doran, though, the video captured exactly the kind of issues the protesters are complaining about.

“It’s telling that he didn’t deny any of it,” she said. “We wish the USDA would come and confiscate all the monkeys. What’s going on here is obscene.”