Henare has decided to part ways with the four-time champions after two years at the head coaching position.
As a player, he won a championship with the Breakers in 2011 and was the first player in Breakers history to have his number retired by the club.
New owner Matt Walsh said Henare was set in his decision.
"Paul was offered a contract extension during the season which he turned down and I have since been in further discussions with him, but he has made the decision to move on."
Walsh, who took over the New Zealand club a little over a month ago, says Henare's contribution was significant.
"We wish Paul all the best in the future and thank him for his contribution to the club, on and off court."
With the 2017/18 season coming to a close, the Breakers will begin searching for a new head coach.