Following the vote by the European Parliament to extend controls to sites with boiler capacities of 20MW - down from 50MW - the issue will be raised next at a meeting of Europe's Council of Ministers on 25 June.
NFU chief environmental adviser Diane Mitchell said: "The outcome of the vote in the European Parliament was a deeply disappointing one, because of its potential implications for the protected crops sector.
"The NFU remains committed to lobbying for the proposed lowering of the rated thermal input, to below 50MW, to be rejected."
She said the NFU questioned whether IPPC is the most appropriate regime to control emissions from these businesses and "to what extent this proposed change will benefit the environment".
Lea Valley pepper grower and NFU horticulture board vice-chairman Gary Taylor said the directive's bureaucracy and cost to growers was a worry.
A Defra team, which visited his nursery last year as part of the NFU's campaign, estimated his cost of compliance at between £70,000 and £80,000.
Taylor said this was a huge amount for any nursery to find in the current climate.
He added that the need to comply was triggered by a nursery's total maximum boiler capacity, no matter whether it was all used. "We want to see a mechanism that looks at what capacity is used, not at what you have.
"You could find that your boiler and combined heat and power (CHP) plant gets you over the new threshold even if you don't actually use 20MW.
"We fully understand the need to reduce carbon footprints but the IPPC ignores the fact that for much of the time, we are burning fuel but no CO2 is going into the atmosphere - instead the gas is being used within the greenhouse to produce extra weight of crop."
Taylor added that some protected edibles sites with CHP and no more than 4ha of glass could find themselves over the proposed new threshold.