Defence Force chief Lieutenant-General Tim Keating is stepping down from the role, but says Operation Burnham had no influence in his decision.
He won't seek reappointment at the end of his term on June 30.
Keating revealed his decision in an email to staff today, saying it had been his absolute privilege to have served in the role since January 2014.
Keating's announcement comes during close scrutiny over the Defence Force's admission last month that photos in Nicky Hager and Jon Stephenson's book Hit & Run were accurate - reversing the Defence Force's initial claim that it never operated in the photographed areas in the Afghanistan operation.
"One thing I wish to place on record is that my departure had nothing to do with the recent spurious publicity about Operation Burnham – a 2010 NZSAS operation in Afghanistan.
"The allegations contained in the book Hit & Run effectively alleging war crimes and indiscriminate destruction of property are wrong.
"There has been no recent 'admission' by the NZDF which reverses the position we carefully set out in March of last year when the book came out.
"The conduct of our ground forces during Operation Burnham was exemplary and nothing has changed that fact," he said in the email.
The New Zealand Defence Force (NZDF) referred all questions to Defence Minister Ron Mark's office.
Mark said in a statement that there was a big programme of work ahead for the NZDF and he believed now was the right time for the next leader to "stand up, be part of the decision-making process and own those decisions".
Keating had served "incredibly well" as Chief of Army and Chief of Defence Force.
"Tim is a dedicated military professional who has achieved great things during his career. The NZDF is in good shape due largely to his hard work and commitment. I'd like to thank Tim for his service to New Zealand and I wish him well in his future endeavours," he said.
Mark said Keating had had an outstanding career which included success as the Commanding Officer of 1SAS, CRIB 6 in Afghanistan and 2nd Land Force Group in Linton.
The State Services Commissioner has begun the recruitment process for Keating's successor.
Stephenson said today he was not lamenting Keating's departure and there would be others in the NZDF who would feel the same.
"He has shown a serious lack of moral leadership and let down the troops who were under his command, many of whom have served New Zealand honourably."
Stephenson said there were many personnel who had served in Afghanistan who struggled to put their experiences into context or had lost friends and colleagues.
"The fact that the public's been lied to for so many years about so many things that have happened in Afghanistan is preventing a lot of those soldiers from grieving and moving on."