DoC expected to recover this through savings made over the next three years.
"Change is never easy and the past few months have been unsettling for staff.
"The new structure is an important step forward, and will see DoC working more in partnership with others to protect the special places and wildlife that New Zealanders value."
Mr Morrison said DoC had about 180 vacancies going into the restructuring process and the organisation still had about 250 new permanent positions to fill.
"Some vacancies are currently filled by temporary staff and they will now have the chance to apply for full time work. We will also be looking for new staff who want the opportunity to work with DoC."
The restructure was confirmed in May and takes effect on September 2.
The changes streamline the department's current 11 conservancy districts into six new conservation delivery regions.
The Greens said DOC's "confused purpose and clumsy structure'' had led staff to vote with their feet and leave.
"The restructure has been bad for morale and as a result, the Department appears to have haemorrhaged staff,'' said Green Party conservation spokeswoman Eugenie Sage.
She said DOC's practical conservation work would take a hit until the vacancies were filled.