These expenses do not include a payment of an undisclosed sum - understood to be a six-figure amount - to Mr Stephenson in a settlement that included a statement by Defence expressing "regret".
Mr Stephenson had claimed $500,000 in damages.
Mr Stephenson engaged two lawyers. He said he did not believe there was a need for the Defence Force to spend such a large sum.
The journalist sued the Defence Force chief at the time, Lieutenant General Rhys Jones, and the force, claiming he was defamed in a press release Mr Jones issued in May 2011.
The release was in response to a Metro magazine article by Mr Stephenson about the handling of detainees in Afghanistan and whether SAS troops had passed prisoners to authorities known to use torture.
The article won an international award and a New Zealand award for investigative reporting.
The journalist argued that words in the press release meant that he had made up an account about visiting an Afghan police Crisis Response Unit base in Kabul and interviewing the commander there.
A trial in Wellington in 2013 resulted in a hung jury.
The Defence Force and Mr Jones now accept Mr Stephenson did go to the base and did interview the commander.