The spokesman would not reveal the nature of the ill-treatment or the assault, the extent of injuries incurred or if any charges had been, or were likely to be, laid. However, he confirmed the military police were conducting the investigation.
"The Navy has zero tolerance of violence of any kind, however, from time to time individuals do not meet our high expectations.
"When this occurs we take all allegations seriously and investigate thoroughly."
In November, naval rating Iosefatu Siulai was sentenced to community work and supervision and ordered to pay $1500 for his assault on two men after a navy function in Auckland.
Last year naval rating Grenville McFarland pleaded guilty to the manslaughter in 2013 of student Tarun Asthana, 25, who died after being king-hit outside the McDonald's outlet at Britomart.
The Devonport Naval Base is the home of the Royal New Zealand Navy and houses all its operational units including ships as well as training and support services for personnel.