National Librarian Penny Carnaby has resigned early, just before the library is absorbed by the Department of Internal Affairs.
Ms Carnaby says her last day will be 17 December, although her term was due to end on 31 January.
Internal Affairs advertised the job last week as part of the move to the new organisation.
Under the changes, whoever is appointed National Librarian will be a third-tier manager within the department.
The change, which includes bringing Archives New Zealand within the department, has been criticised by the Labour Party for undermining the roles of both organisations.