With the introduction of the 1999 Apple and Pear Marketing Board Restructuring Act, a number of "Industry Good" functions were transferred from the NZ Apple and Pear Marketing Board to Pipfruit Growers New Zealand Inc. (PGNZI). These functions included much of the Research and Development, Integrated Fruit Production programme and Technology Transfer components of the industry.

To ensure the research components of the industry were able to be developed in a commercial manner, in January 2000 PGNZI established a limited liability company, NZ Pipfruit Ltd, to manage the grower's R&D and Technology Transfer functions. The establishment of the company, with obvious very close ties with PGNZI left the latter organisation clear to concentrate on the policy and representative issues of the industry while NZ Pipfruit Ltd could concentrate on the technology issues.

In January 2004 the developing overlap of roles resulted in the merger of PGNZI and NZ Pipfruit Ltd to form NZ Apples & Pears Inc.

In July 2004 the members voted to extend the membership groups of NZ Apples & Pears Inc. to include non-grower packers, coolstore operators, marketers and associates such as horticultural suppliers and consultants.

One hundred percent owned by NZ pipfruit growers and working for the benefit of the NZ pipfruit sector. The majority of the company's funding comes from the industry levy and the structure provides for clear accountability for expenditure.