The NFU said growers in the scheme cut their tax bills by an average of £14,000 a year, yet many were "frightened" to sign up.
Commercial director Chris Plackett of FEC Services, which runs the scheme for the NFU, said: "Some growers have been put off because they think it is too complex.
"They are frightened they won't meet the energy-saving targets," Plackett said. "And while the targets are challenging, most growers are able to meet them and make significant savings."
Last year 182 nurseries saved £1.9m using the scheme, he added. Growers could seek advice from groups like the Carbon Trust and the NFU but needed to "get their skates on".
Applicants must sign up by the end of July to the scheme, set up by the Government in 2001, he said. Growers send meter readings to FEC Services to calculate savings.
The NFU lobbied the Government to ensure growers of protected horticultural crops that met energy saving targets would get 80 per cent off their bills.
"The current discount arrangements end in 2013 and people wanting to join or rejoin must apply as soon as possible," said Plackett.
Gary Taylor, managing director of Valley Grown Nurseries and vice-chairman of the NFU horticulture board, said savings could be made without spending money.
Valley Grown Nurseries in Roydon, Essex, spent £30,000 on lagging tanks but saved that amount within four months, he said. He had also improved IT to pinpoint savings."There are things people can do to optimise the performance of their computers and their computer settings, which have a significant effect.
"Some growers have the tools in place but don't necessarily use them to their potential."
Contact FEC Services on 024 7669 6512