The president said in a tweet that Zinke would leave the administration at the end of the year.
Zinke's personal conduct and management decisions have spurred at least 15 investigations, several of which have been closed.
The most serious one, which the Interior Department’s acting inspector general referred to the Justice Department, focuses on whether the secretary used his office for personal gain in connection with a land deal he forged in Whitefish, Montana, with Halliburton Chairman David Lesar and other investors.