There were concerns that it would give the commission too much power and leave EU countries without any leeway to tailor the new rules to their needs. Following the commission's refusal to withdraw its draft text and table an improved one, Parliament closed the first reading. The draft text was rejected by 650 votes to 15.
NFU horticultural adviser Chris Hatfield said: "This is a huge mess and the worst of all possible outcomes. Not only do we have no changes made by MEPs, going forward the second reading is always much harder to influence. The second reading will start on the basis of the council position and MEPs will have much less opportunity to put forward amendments.
"Industry success going forward will be more dependent on getting support from member state representatives, which is fine if everyone agrees on an issue. But if there is any difference in opinion of stakeholders, we know the member state position tends to only reflect the most common position.
Plants for Europe owner Graham Spencer said: "It seems not to be the best outcome. By finalising the first reading, Parliament has said 'this is too hard for us to put right', whereas pushing for the amendments that the stakeholders suggested and were proposed by MEPs could have changed the regulation into something the industry could work with.
"Consequently, the commission could push through its text unless council kills it, which seems unlikely, and we would end up with a regulation that includes most if not all of the issues that worried us in the first instance.
Binsted Nursery director Martin Emmett said: "The analysis is correct. This topic has now gone into EU constitutional deep water. I am seeking further guidance."
Campaigners have said PRM could cost nurseries thousands because it would require more work registering and describing plants.
Plant Heritage plant conservation officer Mercy Morris said: "It's impossible to predict what will happen next. It would be very disappointing to have the opinions of our elected representatives ignored. I urge everyone to maintain the cooperation between different areas of UK horticulture that has served us well so far, and be vigilant for developments."