The European Crop Protection Association (ECPA) was responding to allegations that there was "strong evidence" of contacts between the association and the executive over the ongoing trade talks between the EU and U.S.
Four Brussels-based NGOs also said the association enjoyed a "cosy relationship" with the Commission.
The NGOs are: Corporate Europe Observatory, Friends of the Earth Europe, WeMove, and LobbyControl.
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A letter, seen by this website, sent to the ECPA from the NGOs said that the association's plans for regulatory cooperation on pesticides would "weaken" the EU's protective laws.
The letter goes on, "We take the view that your demands for TTIP would increase the amounts of pesticide residues on food and the use of carcinogens in Europe."
It adds, "In addition, they could further weaken public access to information on pesticides and increase industry influence in decision making, thus undermining democracy."
The NGOs say they have now nominated the association for their "Democracy for Sale" awards, which "expose collusion between business groups and the commission" over TTIP.
ECPA responded with Graeme Taylor, its director of public affairs, robustly rebutting the allegations in a letter to the NGOs.
It reads, "ECPA values the importance of democracy. This is why, as an organisation, we participate fully in the democratic process as we, you and any other interested stakeholder is fully entitled to.
"There are many definitions of democracy, but if you look at it as being an organisation or situation in which everyone is treated equally and has equal rights, then we have an obligation - and make no secret - of the fact that we represent the interests of our members, much in the same way as your respective organisations represent yours.
"I'm not sure how you can make the leap from us legitimately representing our interests, engaging in dialogue and urging the EU and US to adopt a framework for pesticide regulation that is both predictable and robust - to accusing us of collusion.
"It's a jump that would be like us accusing NGOs of collusion if they receive funding from the European Commission and then go on to successfully achieve an outcome that's in their favour."
The letter adds, "Constructive dialogue, and differing opinions, are a healthy part of democracy. We recognise there are concerns about pesticides and these are concerns that we are happy to address in an open and honest debate.
"In fact, we are currently planning an event in November where we will encourage parties from all sides of the argument to take part - we hope we can count on your participation.
"There are different reasons for the existence of all of our organisations, and for us it's to ensure our members can continue to provide the tools farmers need to produce a safe, sustainable and affordable supply of food for the growing world population: I'm sure that is in all of our interests."
ECPA said it "strongly supports" TTIP and the potential the agreement has to "boost agricultural innovation as well as job and economic growth on a global scale."
Taylor told this website, "The allegations are not substantiated in any way. As with any issue potentially affecting our sector we have made representations to the Commission - our position on TTIP has been made public."
Anna Gatt Seretny, communications manager for ECPA, added, "Like every other party we have engaged and voiced our opinion during the TTIP negotiations."