The rise coincided with the implementation of the force's new restricted disclosure system, which the NZDF said meant the high figures weren't necessarily because there were more incidents.
Rather it showed an "increased confidence in our organisation to take complaints seriously and respond appropriately," a spokesman said
"NZDF is confident that a decline in actual offending and inappropriate behaviour will occur."
In early 2016, Operation Respect was launched as part of the NZDF's efforts to "eliminate harmful and inappropriate sexual behaviour" within its ranks.
As part of this a Sexual Assault Response team was introduced on June 30, 2016 along with a new, restricted disclosure system for its members to report any incidents.
The NZDF said its progress was being governed by a steering group that includes external members.
The changes followed an independent, external review of inappropriate behaviour in the Royal New Zealand Air Force, which highlighted there was a culture of sexist attitudes and behaviours, in particular against women.
Last year, four men lodged complaints, compared to a total of nine across the previous nine years.
The NZDF spokesman said its work to date has raised awareness that the issue was not limited to women and it was working to "reduce stigma and hesitancy for men to report".
Most of those who laid a complaint were young in 2016, 28 under 30 [years of age], including eight women and one man younger than 20. Only six were over 30.
The ages of the alleged offenders weren't divulged, but figures showed six were officers and two were senior non-commissioned officers.
Director of Tiaki Consultants Dr Kim McGregor worked on the Airforce Culture Review in 2015 that led to Operation Respect's launch.
The rise in reported incidents illustrated the system was doing what it was intended to do, she said.
"What was hoped for was a confidence for people to come forward, and if there's been an increase in reported incidents, it's probably early days, but it could suggest the system is working."
In time McGregor hoped the NZDF's focus on sexual violence prevention would lead to a decrease in actual incidents.
In 2016 two of the complaints laid resulted in a police warning, two in police prosecution and two were seen at a Military Police Summary Trial.
Eighteen were still under investigation; two were not to be investigated further; and 10 others were reported as restricted disclosures, meaning the complaint was heard and support given to the person involved without the case being escalated in a formal report to management or passed onto the New Zealand Police.
Debbi Tohill, executive director Rape Prevention Education, said it was important for people to be able to access help when they need it and "in a safe and non-judgemental way".
"Zero tolerance for all forms of sexual violence and abuse is also crucial."
There were a number of NZDF cases reported on last year, including that of the navy commander Philip Wiig who was found guilty of groping a more junior officer and was dismissed from service.
The court found he had performed in a manner that undermined the NZDF's core values and struck "at the heart of fitness to command".
Breakdown of sexual assaults/harassment complaints in past decade
2016:
Total sexual assaults/harassment complaints: 41 (including 1 sexual violation/rape)
Men: 4 Women: 36 Undisclosed: 1
2015:
Total sexual assaults/harassment complaints: 26 (including 8 sexual violation/rape)
Men: 0 Women: 25 Undisclosed: 1
2014:
Total sexual assaults/harassment complaints: 18 (including 3 sexual violation/rape)
Men: 2 Women: 16
2013:
Total sexual assaults/harassment complaints: 16 (including 2 sexual violation/rape)
Men: 1 Women: 14 Undisclosed: 1
2012:
Total sexual assaults/harassment complaints: 17 (including 1 sexual violation/rape)
Men: 1 Women: 16
2011:
Total sexual assaults/harassment complaints: 15 (including 2 sexual violation/rape)
Men: 0 Women: 9 Undisclosed: 6
2010:
Total sexual assaults/harassment complaints: 25 (including 4 sexual violation/rape)
Men: 1 Women: 17 Undisclosed: 7
2009:
Total sexual assaults/harassment complaints: 26
Men: 1 Women: 21 Undisclosed: 4
2008:
Total sexual assaults/harassment complaints: 21
Men: 2 Women: 18 Undisclosed: 1
2007:
Total sexual assaults/harassment complaints: 24 (including 2 sexual violation/rape)
Men: 1 Women: 21 Undisclosed: 2
2006:
Total: 28 (including 3 sexual violation/rape)
Men: 0 Women: 28
