Buffer zones would also be mandatory to protect aquatic environments and drinking water from pesticides.
The Soil Association backs the EU's bid to cut the use of chemicals it says can cause cancer and infertility.
The association's policy director, Peter Melchett, said organic farmers had proven that crops could be grown with minimal use of pesticides.
"The vast majority of farmers don't use these chemicals on a regular basis anyway and those few farmers who do use them can find alternatives," he said.
Italian Green MEP Monica Frassoni said the vote was "a victory for the Greens and environmentalists, who managed collectively to resist enormous pressure (from industry)".
But National Farmers' Union deputy president Meurig Raymond said members "could be facing a difficult future with our agriculture and food production seriously threatened".
It is ludicrous that we would bring in a law that would put our crops in real danger
Robert Sturdy MEP
"The lack of sound science behind the plans is a major concern," he said.
"We cannot support measures which reduce the tools available to farmers and growers to produce crops and that could ultimately jeopardise future food supply and security."
British Labour MEP Glenis Willmott however pointed to an important safeguard clause in the package. It says a substance needed to tackle a serious danger to plant health can be approved for up to five years, even if that substance does not meet the new safety criteria.
Changes in the way pesticides are authorised for use on crops are part of an EU goal to halve the use of toxic products in farming by 2013.
The plans include assessing products for protecting plants on the basis of "perceived hazard", instead of scientific evidence.
The proposals have already been scaled back after Europe's pesticides industry warned they would remove from the market products that had been used without problems for years.
Most pesticides currently on the market will be valid until at least 2015, giving pesticide manufacturers time to reformulate their products.
Even so, Environment Secretary Hilary Benn said the regulations could hit agricultural production in the UK without producing a recognisable benefit to human health.
"We are being asked to agree to something here when nobody knows what the impact will be," he said.
"While we have managed to secure some improvements surrounding the use of certain pesticides, the UK does not support these proposals."
Conservative MEPs say almost a quarter of produce will be lost in the UK alone if the plans go through, including the total carrot yield and 20% of cereal production.
Along with Labour counterparts, they are calling for a full impact assessment of the proposed changes before the measures are approved.
Conservative Robert Sturdy MEP said: "We must have safer pesticides that are used responsibly but banning products that are safe when used correctly will add to already volatile food prices and food shortages.
"Food security is already becoming a pressing issue, so it is ludicrous that we would bring in a law that would put our crops in real danger."
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