The 26-year-old Academy graduate, who has been with the U's for over 10 years, is out of contract this summer and has turned down the terms on the table, leaving him free to find a new club.
Boss Joe Dunne told Colchester's official website: "John White has decided not to continue with us. His representatives contacted me to say that he wouldn't be signing the contract we offered.
"It was a contract that would have seen his salary reduced but that is something that is happening pretty much across the board and we had hoped it would be enough for him to stay.
"We fully understand that he would now like to see what else is out there for him and we wish him all the best wherever he plays."
White made over 250 appearances for Colchester since making his first-team debut for the Essex outfit in 2004.