National Basketball Players Association Executive Committee President Derek Fisher said in a statement the vote by player representatives was unanimous.
"Today was a day of change for our association and our union," Fisher said. "We held a meeting with the board of player representatives, with many different groups of players represented."
Hunter -- who has led the union since 1996 -- had been on indefinite leave since Feb. 1 following a review that turned up evidence he hired family and friends.
The review turned up no illegal behavior but raised questions about Hunter's travel and other expenses.
"We wa-nt to make it clear that we are here to serve only the best interests of the players," Fisher said. "No threats, no lies, no distractions will stop us from serving our membership. We do not doubt this process will continue in an ugly way ... This is our union, and we have taken it back."