Nearly 4,000 beagle puppies were rescued from the Envigo RMS LLC breeder, which sold them to scientific laboratories in Cumberland, Virginia.
In May, the US Department of Justice sued the company for animal abuse.
The researchers found that animals were euthanized instead of receiving veterinary attention for simple health problems, pregnant females were denied food or offered food with worms, mold and feces.
The animals will be transported to rescue organizations across the country to rehabilitate them and find them a permanent home.