AgResearch, the largest Crown research institute, has reported a net loss of more than $8 million.
AgResearch achieved a before tax surplus of $2 million, but changes to depreciation rules turned that into a deficit.
It says revenue was below budget mainly due to a slower than expected start to the Government's primary growth partnership research funding programme
Rejection of wool levies by farmers also forced it to reduce some research activities and cut staff.
Another CRI, the forestry research institute Scion, made a higher than forecast pre-tax profit of more than $3 million.
But a depreciation tax adjustment converted that to a net loss of almost $1 million.