Gordon cited growing strain with board members over the group's management style and future operations.
"I believe that any organization that's going to be effective will only be effective if the board and the CEO are aligned and I don't think we are aligned," Gordon said. "This compromises the ability of the board to be as effective as it can be."
He spoke by phone from Los Angeles, where he had just attended the taping of the NAACP Image Awards.
Dennis C. Hayes, general counsel of the Baltimore-based National Association for the Advancement of Colored People, is expected to serve as interim president, Gordon said.
Hayes filled the same role after Kweisi Mfume resigned the presidency in 2004 after nine years.
Hayes said that while the NAACP is an advocacy organization, it needs to be more focused on service and finding solutions.
"I'm used to a CEO running an organization, with the board approving strategy and policy," Gordon said. "But the NAACP board is very much involved."