"We direct (that) no zoo shall permit any further breeding of animals," Chief Justice Y.K. Sabharwal said.
The order from India's top court came in response to a petition filed by PETA (People for Ethical Treatment of Animals) which accused zoos of carrying out unsystematic breeding, endangering the animals.
The group said zoos were violating a cap on the number of animals, such as tigers and deer, permitted to be bred in captivity and the overcrowding had left zoos ill-equipped to look after the animals.
"Most of these animals in zoos are also genetically unfit for breeding and their offspring can never be released in the wild," PETA counsel Raj Panjwani said.
The group said only 18 of the country's 250 zoos had a proper, planned breeding programme.
The court ordered an immediate halt to all breeding programmes in the country's zoos, which hold around 41,000 animals. They also called on local authorities to respond to PETA's request for experienced veterinary units in zoos.