"Some of these cages had holes in them, some of them were sort of loose on the bottom allowing these monkeys to get stuck," the Humane Society investigator said, referencing video of a monkey with its arms trapped in holes in their cages.
Another alleged violation shown in the investigator's 2008 footage: Sedated chimpanzees, that are five times stronger than humans, apparently being transported without protection or restraint, a practice Fakier said dates back to her tenure at the New Iberia Research Center.
"That's exactly how we transported," Fakier said as she viewed video of two lab employees carrying a sedated chimpanzee by its arms and legs and laying it in the back of a van. "We're in the back with another anesthetized chimp, who could wake up at any moment. The direction was if he wakes up, run.
"My building was close to a day care," Fakier added.
One chimpanzee at the New Iberia Research Center is named Siafu. Fakier suspected that the chimp was trained in American Sign Language.
"I tried several times to get him help," Fakier said. "He'd get so frustrated and so aggravated because he was trying to sign and they didn't know what he was saying."
The National Institutes of Health gave the New Iberia Research Center nearly $18 million in federal funds for chimpanzee research between 2000 and 2009. It also declined "Nightline's" repeated requests for an on-camera interview in favor of a statement that, in part, said, "Thanks to research involving primates, countless lives have been saved. For example, primates were critical to the development of vaccines for hepatitis A and B, now common pediatric immunizations. In addition, the chimpanzee is integral to current efforts to develop vaccines for hepatitis C, which globally affects more than 170 million people."
The New Iberia Research center also stated tha their animal care and use program was last reviewed by the U.S. Department of Agriculture in September of 2008, and by the NIH's Office of Laboratory Animal Welfare in 2009, and that these reviews found all programs to be in compliance with the Animal Welfare Act. But the USDA told ABC News today that they did not give the lab a clean bill of health.
The Humane Society investigator said her days at the lab were difficult.
"I tried as much as I could to give the chimps some one-on-one attention," she said. "The least I could do is provide some sort of vocal or physical comfort to them. What kept me going was knowing that this video will be released."
As for Fakier, she says she will wait for her day in court.
"I have lost faith in the system. And this is a system that I had defended over the years. My fear is that's what's going on around all the primate facilities around this country. And if that's the case, then a tragedy is occurring right now. Flat out a tragedy is occurring."
World famous primatologist Jane Goodall reacted to the HSUS investigation in a statment posted on the Humane Society's Web site. "In no lab I have visited have I seen so many chimpanzees exhibit such intense fear," she wrote after seeing the undercover video taken at the New Iberia Research Center.
As a result of the ABC News investigation and the Humane Society of the United States video, the Office of Laboratory Animal Welfare, part of the National Institutes of Health, told ABC News it is investigating the allegations made against the New Iberia Research Center.