It showed 87 per cent of employers reported that none of their employees were union members.
That number was 90 per cent for small businesses – firms with fewer than 20 employees – and 60 per cent for large businesses.
National's workplace relations spokesman Scott Simpson said while support for the union movement has been dwindling, the unions have remained a core element of the Labour Party.
"That explains why we're in the midst of the worst outbreak of strikes in decades."
Workplace relations Minister Iain-Lees Galloway deferred comment to the unions.
Council of Trade Unions (CTU) President Richard Wagstaff said the numbers were disappointing.
"We really believe working Kiwis would get a much better deal if they were united and empowered through belonging to their union."
He said the most common reason for people not joining unions was because people don't realise there is a union for them, or they don't know the benefit.
E tū Assistant National Secretary John Ryall said international experience shows that low level of union membership corresponds with the low level of collective bargaining.
MBIE's report shows employers with union members on staff were more likely to describe their current relationship with unions as positive rather than negative.
The MBIE report showed that almost one in five employers had said they had undertaken reviews to check that men and women in the same role were paid equally.
"However, few employers reported that the business had undertaken training about potential gender bias, 4 per cent, or sought advice regarding the Equal Pay Act 1972, 5 per cent."
Minister for Women Julie Anne Genter said it was encouraging that 20 per cent of employers were taking action to ensure women are paid fairly.
"There's obviously an opportunity for more employers to do the same," she said.
"Addressing potential gender bias means that everyone's talents can be fully utilised. This benefits everyone, especially business."
• An earlier version of this story wrongly said that 90 per cent of Kiwis working in business were not members of a union.
Key numbers:
-Two-thirds of hiring employers used a trial period
-One-quarter of hiring employers who used the trial had dismissed an employee
-One in 10 employers had taken on an intern in the last 12 months
-Almost 60 per cent of employers of interns reported they had paid their most recent intern
-Close to one in five employers had undertaken reviews to check that men and women in the same role were paid equally
-Almost 90 per cent of employers said they had no employees in unions
-One quarter of employers were paying the adult minimum wage to one or more employers
-Six out of 10 employers with job vacancies had difficulties finding staff to fill vacancies
-Seven out of 10 employers agreed that migrants make an important contribution to New Zealand's economy.