The Ministry of Agriculture and Forestry says the horticulture sector was a surprise exclusion from the first year of the primary growth partnership with the Government.
The partnership aims to invest up to $140 million per year in primary sector research and innovation.
Five grants have been approved to a total of $368 million over the next five to seven years, including $164 million from the Government.
They represent the wool, arable, forest, meat and dairy industries.
MAF director-general Murray Sherwin says there have also been some interesting applications from aquaculture and marine fisheries.
But he is disappointed the horticulture sector is not yet in the mix.
Horticulture New Zealand says the industry is keen to tap into the partnership, but with 22-sector groups it is proving hard to find something that meets everyone's needs.