Milling of native timber is controlled under the Forest Act 1949 through forest management plans or permits.
MPI northern compliance manager Greg Keys said felling native timber without consent threatened the sustainability of indigenous forests.
"In this case, because of the very slow growing nature of tawa trees, replacement will likely take many decades," he said.
"This sort of blatant offending is unacceptable and the ministry is pleased to see the courts taking a strong stance in this case.
"Mr Cody was well aware of his obligations under the Forests Act as he was a registered sawmiller between 1995 and 2000 during which time he submitted sawmill returns relating to the milling of indigenous timber."