Flo the chimpanzee bounds about her enclosure, hurls a rubber ball then stares quizzically at the New Mexico green chili pepper that will be her morning snack.

It has been a long time since Flo was on exhibit at the Memphis Zoo, even longer since she learned to smoke cigarettes during a stint with the circus. Most recently, she was a research chimpanzee here in New Mexico, part of an expansive biomedical testing program for hepatitis C and H.I.V.

At the moment, though, she is out of a job — but perhaps not for long.

Flo and the 185 other chimpanzees who live at the Alamogordo Primate Facility at Holloman Air Force Base have not been research subjects for nearly a decade — part of an agreement between the National Institutes of Health and the military, which prohibits using the animals for biomedical tests on the base.
But recently, the health institute decided it wanted to use the chimp colony for medical research again, primarily to help develop the elusive hepatitis C vaccine. This past June, the institute began shipping some of the animals by special trucks to the Southwest National Primate Research Center in San Antonio and plans on moving the remaining chimpanzees by the end of 2011.

The move has spurred outrage among animal rights advocates, primate experts and politicians, who say the chimpanzees — many of them middle-aged and elderly — should get to live out the rest of their lives in peace after years of invasive research. It has also cast a fresh light on the debate over the tipping point between science and ethics, with everyone from the legendary primatologist Dr. Jane Goodall to Gov. Bill Richardson of New Mexico weighing in.
“These chimpanzees have given up their freedom, if not their natural environment, their bodies, their health, their children to research,” said Laura Bonar, program director for Animal Protection of New Mexico, which wants the government to turn the Alamogordo facility into a retirement sanctuary for the chimps. “And at the end of their lives, we can give them something back.”
For the health institute, though, the Alamogordo chimpanzees represent an invaluable resource. As per the agreement with the Air Force, biomedical research cannot be conducted on the animals. That agreement was forged after the institute acquired the chimpanzees from the Coulston Foundation, an infamous New Mexico research laboratory that was found by federal officials to have abused and neglected the animals.
In 2001, the institute gave the private Charles River Laboratories a 10-year contract to provide medical care to the chimps, most of whom have been infected or exposed to hepatitis C and H.I.V. through prior research.
These days, chimps like Flo, who at 53 is the oldest of the Alamogordo colony, spend their days living in small groups in geodesic domes: foraging for food, swinging from structures and whooping greetings at visitors and one another.
Harold Watson, who heads the chimpanzee research program for the National Center for Research Resources, said that with the end of the contract, it only makes sense to use the chimps for their original purpose. The research — which will most likely entail drawing periodic blood samples, liver biopsies and in some cases inoculations of hepatitis C — will be carefully monitored, he said.
“I think people envision pictures of monkeys with electrodes in their heads,” Dr. Watson said. “This is not what we’re talking about.”
The history of primate research, however, has been long and controversial. Because of their genetic closeness to humans, chimpanzees are considered well-suited for studies of how various infectious diseases or psychological environments might affect mankind.
But some have questioned whether that research has yielded any substantive breakthroughs, and the United States is currently the only developed country that continues large-scale confinement of chimps in laboratories, according to the Humane Society of the United States. Supporters of the research say the animals have been critical in the development of hepatitis A and B vaccines.
Pending Congressional legislation known as the Great Ape Protection Act would retire about 500 federally owned chimpanzees currently in laboratories to permanent sanctuary. The Alamogordo colony traces its lineage to the Air Force’s space chimp experiments in the late 1950s. A decade later, the toxicologist Frederick Coulston set out to build the world’s largest captive colony of chimpanzees for research, in New Mexico. His foundation’s tenure was marred by charges of severe mistreatment.
That legacy still haunts the health institute, which got 288 of the chimpanzees around 2001 and has tried to distance itself from the Coulston Foundation.
John Gluck, a professor emeritus of psychology at the University of New Mexico, who has visited the Alamogordo colony at least four times since the 1970s, is worried what a move to Texas would mean for the animals’ physical and mental health, particularly given “the tremendous price” paid by most of the chimpanzees while research subjects of the Coulston Foundation, he said.
“N.I.H., in general, is a place I respect,” Dr. Gluck said. “But it seems to me that they’ve lost both their ethical and scientific compass here.”
Governor Richardson has also urged the institute to reconsider, and Dr. Goodall wrote to the institute that the chimpanzees “will surely suffer considerable physical and emotional distress from this plan.”
Dr. Lon Lammey, the director of the Alamogordo primate facility for Charles River, the private contractor, disputed the notion that the move would be harmful, and said he was “confident the animals would continue to receive optimal medical care.”
Despite the mounting pressure, the institute has shown little sign of changing its plan.
Some 15 miles from the base, a separate group of 82 chimpanzees are also waiting to be moved, but to a lush Florida sanctuary run by Save the Chimps, a rescue group.
The animals were part of a larger group handed over to the rescue organization by the Coulston Foundation after its demise and have gradually been moved to Florida over the past few years. Save the Chimps wants the institute to permanently retire the rest of the Alamogordo chimpanzees to a sanctuary as well.
At the old Coulston facility, which has been transformed into a temporary sanctuary itself, a 13-year-old chimp named JJ clutched a bundle of security blankets while readying for lunch. As a worker placed bushels of fruit in the enclosures, the chimpanzees began to yelp in unison, their cries carrying across the high desert.

A version of this article appeared in print on September 2, 2010, on page A23 of the New York edition.