Draft legislation tabled by the Commission proposes to open up competition for manufacturers of organic waste-based fertilizers in a market currently dominated by non-organic fertilizer companies.
Supporters of the proposed rules, a revamp of the 2003 regulation, say such changes will open the door for innovation.
But, speaking at an event in Parliament on Wednesday, Dominique Dejonckheer, of farmers' organisation Copa-Cogeca, expressed "deep concerns" at the planned legislation which is currently being considered by MEPs.
She said, "Our concern is that this new regulation will weaken existing rules because transparency on the use of mineral fertilizers will be reduced. This is not a good thing for farmers."
Dejonckheer added, "The message we would like to convey is: keep the best of the 2003 regulation."
She was addressing a debate, 'Forum on Fertilizers', organised by Fertilizers Europe, the body representing the majority of Europe's fertilizer producers, which looked at the likely impact of the draft legislation.
In response, German centre right MEP Peter Jahr, who hosted the discussion, told Dejonckheer, "I want to assure you that we in the Parliament want to improve the Commission's proposal."
One of the key issues, the hearing heard, is the possible consequences for environmental and human health and the permissible limits of cadmium in phosphate fertilizers.
Some in the fertilizers industry fear that if the maximum level of cadmium becomes too strict, the price of phosphate, mainly from Russia, will increase sharply.
EPP group member Jahr said, "As a farmer, I welcome the proposal and, as a politician, I can see the opportunity for harmonisation. However, there are also some areas in the regulation that need to be addressed."
The event heard that the draft does not take into account research showing that phosphate fertilizers containing 80mg/kg do not lead to cadmium accumulation in the soil.
Jahr said any final decision on the maximum level of cadmium, and other heavy metals, "must be based on science and not politics."
Another area of concern he highlighted is the definition of mineral fertilizers and he believes mineral fertilizers need to be clearly defined to ensure that they meet farmers' expectations.
Given that fertilizers contribute to 15 per cent of global food production, the importance of new regulation, he said, should not be under-estimated.
Another speaker, Thomas Mannheim, of EuroChem, a Swiss-based fertilizers company, said, "The regulation is a mix of everything but what we need is a level playing field for different fertilizers."
Udo Hemmerling, deputy Secretary General of the German Farmers' Association (DBV) stressed the "equal importance" of both organic and mineral fertilizers.
He also agreed on the need for a "scientific base" in deciding levels of cadmium in fertilizers and said the new law "must maintain the quality" of Europe's fertilizers.
The meeting heard that without mineral fertilizers, 50 per cent of the world "would go hungry."
The draft regulation has been sent to the Parliament and Council for adoption. Once adopted, it will be directly applicable, without the need for transposition into national law, after a transitional period allowing companies and public authorities to prepare for the new rules.