The European Commission (EC), as part of a series of changes it has adopted to update the Integrated Pollution Prevention and Control (IPPC) Directive, is proposing to reduce businesses' thermal input threshold - the capacity of their boilers - from 50MW to 20MW.
The NFU fears that at least a dozen large glasshouse facilities could be affected by the proposals.
NFU horticulture adviser Chris Hartfield said: "This is not about energy use but boiler capacity. It's like owning a 150mph sports car that you never drive over 50mph. It would also include growers with two boilers of different sizes."
The NFU has described the proposals as "lumping (horticultural) businesses in the same bracket as power stations" and plans to lobby hard in Brussels to influence the discussions taking place on the Directive. Hartfield said: "We are here to protect our members. With the IPPC comes a whole raft of regulatory burden. If we can avoid that (burden) then that's the route we will take.
"The EC has just adopted the proposals and we are in a period of consultation now. The NFU is drawing up a response to put to DEFRA."
Humber Growers managing director Roger Sayer said he fears the number of nurseries affected could be higher than the NFU's estimation.
He said: "I think it will affect a lot more nurseries than people think it will. I can think of at least 10 or 11 nurseries straight off, so I think it will be a fair proportion.
"Most glasshouse nurseries would not use more than 20MW but it's not about what you use - it's what you have the capacity for. We have one nursery where we have several boilers - including a gas, a coal and a straw-burning one - so we have three times the capacity that we need. We would definitely fall under these regulations.
"If it was on the capacity that people actually use I would not be so worried. It's definitely going to cost us."
The IPPC was introduced in August 2000 to minimise pollution from various industries.