Helpers dug a hole in the sand by his blowhole so he could keep breathing.
Finally, the tide came in and lifted the whale back to safe waters where he swam free.
"A few boats are still monitoring the whale in the inner Auckland harbour," Project Jonah wrote on its Facebook page. "We left the whale just after 4pm, swimming past Kauri Point in the direction of the Hauraki Gulf. The tide is now going out and we hope the whale continues into deeper water."