The EU directive would make it impossible to register old and new niche varieties and populations based only on an officially recognised description, without official registration and certification.
Franchi Seeds director Paolo Arrigo said: "Europe has a lot more to lose than the UK. In Italy we don't have the standard mass-produced varieties that the UK has. We feel that this will stop diversity and make Europe a homogenous place."
He added: "The EC has some brilliant rules. This is not one of them. It's going to affect biodiversity and regional varieties. The large multinationals will make money but we won't - and who's going to enforce it?"
Franchi maintains 120 seed varieties that were almost lost 10 years ago. "With some of them we make money but a lot of them don't," said Arrigo. "All our varieties are on the EC list, but a small grower in a recession wouldn't have the money to do that."
Soil Association head of horticulture Ben Raskin said: "Access to seed and plant propagating material from diverse varieties is essential for farmers. The proposed regulation goes further than current European seed law, which favours production of uniform varieties and discriminates against less homogenous open pollinated varieties and populations."
The Soil Association said proposed registration and licensing fees could cost it £800,000 a year.