"Charlie and I have agreed that we should move the agency in a different direction," Gov. John Bel Edwards said in a statement Wednesday in which he called Melancon a "tremendous public servant and great friend."
A former congressman, Melancon has clashed with recreational fishermen and Republican U.S. Rep. Garret Graves since taking over the Department of Wildlife and Fisheries when Edwards' term began in January.
Melancon has also run into controversy about programs he cut and changes he made in response to a legislative auditor's report that found shoddy management of agency finances under Melancon's predecessor during former Gov. Bobby Jindal's administration.
Edwards said that although the department will be in a "time of transition," he expects it to continue making "positive reforms" to correct the financial issues from the Jindal era identified by the legislative auditor.
Melancon hasn't commented publicly about his exit, which was first reported by NOLA.com/The Times-Picayune.
In a statement, Graves wished him well and said he looks forward "to working with the new secretary to ensure Louisiana remains the Sportsman's Paradise."