Introduced a year ago, the scheme ensures that those who invest in renewable energy systems such as solar panels get money back from the Government for their efforts to be green.
But the Government has launched a review for fear that the building of too many large solar farms could soak up money it claims is intended for small investors such as residential homes and small businesses.
The NFU fears that the Government could class solar photovoltaic projects above 50kW as large, when they are just the sort of size that is appealing to the food production industry.
NFU chief renewable energy adviser Dr Jonathan Scurlock said: "The NFU is deeply concerned that all solar photovoltaic projects above 50kW are to be included in the FITs review - this will include many agricultural rooftop projects involving as little as £150,000 investment.
"It is imperative that the Government announces its timetable for any proposed changes and the transitional rules that will apply in order to avoid a collapse in confidence among investors.
"This hardly seems like the right way to reward the success that the FITs have achieved so far in bringing new sources of investment into land-based renewables. Alongside the domestic scale, agricultural, industrial and community renewable schemes have a vital role to play in green growth."
The NFU also pointed out that not one solar farm has yet been built in Britain - and only a handful of proposed farms have planning consent to date.
An NFU representative said: "Although a relatively large number of projects have been proposed, the NFU understands that many of these are likely be constrained by the availability of planning consents, grid connections and finance."
Ofgem figures showed that domestic rooftops made up the vast majority of solar photovoltaic projects installed so far, but that overall renewables installations are still below the FITs target rate.