The NFU believed this was not what Parliament intended which "would have damaging widespread implications for nursery growers and the wider horticultural industry" and could have forced growers out of business.
The NFU, with support from the HTA, ratings advisor Turner Morum and the Ornamentals Round Table has been campaigning with Defra and DCLG for the exemption to be reinstated and has now seen success in their lobbying.
Jones said in a written statement to Parliament on 30 March: "Since at least 1928, plant nursery grounds have been treated by the Valuation Office Agency as exempt from business rates as part of the general exemption for agriculture. However, following a recent Court of Appeal decision, the Valuation Office Agency has started to bring into business rates buildings at nursery grounds including structures such as poly-tunnels.
"The exemption for agricultural properties is an important part of the rating system. It ensures that large areas of agricultural land and buildings are not liable to a property tax which could have a significant impact on the cost of farming. I can confirm to the House that the Government’s policy is that land and buildings at plant nursery grounds should benefit from the agricultural exemption for business rates.
"Therefore, we intend at the soonest opportunity to amend the Local Government Finance Act 1988 to ensure both agricultural land and buildings at plant nursery grounds are exempt from business rates. This will return the law to align with the practice followed by the Valuation Office Agency before the decision in the Court of Appeal."
NFU president Meurig Raymond welcomed Jones' statement "and his recognition of the importance of the exemption to the industry at this time of uncertainty".
HTA horticulture head Raoul Curtis-Machin said: "We are delighted with this result, and this is thanks to the NFU, HTA and Ornamental Round Table group for their lobbying efforts. Hopefully this will put an end to the sleepless nights some growers have been having."
But he said there was still a "job to do" in Scotland with some garden centre rate rises almost doubling rate bills compared to similar sites across the border.