BEIJING—China said it would halt harvesting the organs of executed prisoners for transplant beginning next year, following longtime criticism from human-rights groups, though the change could add uncertainty to China’s organ supply.

Chinese officials will stop using the organs of inmates beginning Jan. 1, nearly three years after Beijing first said it intended to stop the program and create a national organ donation system. While China already forbids organ donations without the consent of the donor or the family, critics...