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In a statement posted online, the charity said the techniques used risked "significant damage" to the whale and put the rescuers themselves in danger.
The World Cup winner was travelling by helicopter with ZURU founder Nick Mowbray when the pair spotted the stranded animal on the beach at Mangawhai, north of Auckland, yesterday.
Mowbray told the Herald they were returning from the Bay of Islands when they saw the whale.
Williams is in a relationship with Mowbray's sister, ZURU co-founder Anna Mowbray.
Mowbray said they circled back and landed, telling the Herald the beach was empty when they began their fight to save the animal.
Video of the incident, posted to Instagram by Mowbray's partner Jaimee Lupton, shows Williams and Mowbray pulling the whale by its tail to free it from the sand.
At one point the whale gets the better of Williams, slapping the rangy lock with its tail and knocking him into the surf.
Helped by the surf lifesavers, the group then manhandle the whale through the small breakers and back out to sea.
Whale rescue charity Project Jonah earlier shared news of the rescue on their Facebook page, saying they had offered advice to the lifeguards on how to refloat the whale, identifying it as a false killer whale measuring 4-5 metres.