Dr Jane Goodall said an 18-month-old animal, called Trudy, had been caged in an "utterly inappropriate fashion" at a winter training quarters near Andover in Hampshire.
Ms Chipperfield, 61, and her husband Roger Cawley, 64, deny 28 animal cruelty charges at Croft Farm, Middle Wallop.
Undercover activists from Animal Defenders infiltrated Mary Chipperfield Promotions Ltd last year and shot 800 hours of secret videos.
Dr Goodall had watched film of the chimpanzee apparently being beaten and forced into a cramped cage where it was said to spend 14 hours a day.
She said: "That young chimp has been put through considerable trauma and to leave her there in a cage by herself, hurting and frightened, that to me is very cruel. The chimp was being treated in a way which I would describe as very cruel."
Dr Goodall helps to run four sanctuaries for orphaned chimpanzees in Africa.
The trial continues.
In Wednesday's Independent we wrongly stated that Richard Chipperfield, who was attacked by a tiger in Florida last year, was Mary Chipperfield's son. Neither Richard Chipperfield nor Nigel Wesson, whose arm was bitten off by a tiger last year, is connected with Mary Chipperfield. We have been asked to make it clear that Chipperfield Circus, run by Chipperfield Enterprises Limited, has no business connection with Mary Chipperfield.