It said the low morale was driven by a lack of satisfaction with leadership, and recent changes to regular force personnel.
Labour's defence spokesman Phil Goff said said the level of staff morale in the Defence Force was already very low in 2011/12, and little had changed.
"No wonder the Government hasn't released these documents - in the last financial year there were record highs in attrition of over 20 per cent and record low morale.''
Mr Goff said roughly 2000 of around 8500 regular force personnel had left the force.
"The persistence of high levels of negative feelings is a huge worry and affects the capability and outlook of the Defence Force.
"The National Government has done serious damage to the defence force - not only have key personnel with skills and experience left in their thousands, but a further quarter of experienced military personnel are looking at doing the same,'' Mr Goff said.
Prime Minister John Key said he had recently met the new chief executive and secretary of defence Helene Quilter and she felt morale was improving.
"When we undertook some of the changes there might have been, at the margins, some concerns - change always engenders concern in some people.
"We always want people to be happy in their work and understand where the Government is going - I think for the most-part people generally do,'' Mr Key said.
The survey was taken between October and December last year.
Only 1215 staff, responded, a 49 per cent response rate.
What the report showed:
- Staff morale has remained lower than at any time prior to mid 2011.
- There has been a significant increase in disengagement, with the current quarter higher than early 2011.
- An increase in the number of people saying they intended to leave.
- Only 36 per cent of staff agreed that the pay and benefits they received were fair for the work they do.
- 51 per cent of staff agreed that their pay and benefits would be more favourable in an external organisation.
- 27 per cent of staff agreed that the accommodation assistance they received was appropriate for their situation.
- 42 per cent of staff were satisfied with medical and dental provisions available to them.
- 36 per cent of staff agreed or strongly agreed the Defence Force lacked the equipment it needed to perform well in operations. Thirty per cent disagreed.
- 37 per cent of staff disagreed that communication between senior leaders and staff was good.
- 10 per cent of staff said they had experienced bullying.