Member states have failed to approve a limited extension of up to 18 months of the current authorisation of glyphosate, a controversial substance used for the production of pesticides.
The proposal failed to get the necessary support at a meeting of the EU standing committee on plants, animals, food and feed on Monday.
Twenty member states voted in favour of the extension and only one - Malta - against while seven abstained, including Germany and France.
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The issue will now go to a committee of appeal, possibly on 20 June. The European Chemical Agency will also be asked to give its scientific assessment on the substance.
The failure to secure a qualified majority of EU governments in favour of approving an extension has been welcomed by some.
Greenpeace said the outcome showed that governments "remain sceptical" about the continued use of the weed killer.
But, after Monday's meeting, a Commission spokesperson tweeted, "The responsibility for this decision is on member states. They need to take responsibility."
Concerns about the carcinogenic properties of glyphosate-based herbicides have increased after the World Health Organization’s International Agency for Research on Cancer (IARC) re-classified glyphosate as "probably carcinogenic to humans" last year.
The Greens say there is a need to phase out "this toxic product" which, they say, has "major" damaging impacts both on biodiversity and human health.
Any temporary extension "must be the beginning of the end" for glyphosate, said Greens/EFA group environment and food safety spokesperson Bart Staes.
The Belgian MEP condemned the attempt to "bulldoze through" the re-approval of glyphosate following "heavy" industry lobbying.
Staes said,"While it means an eleventh hour reprieve for glyphosate, this is hopefully only temporary and this should be the beginning of the end. The EU will now have to finalise its assessment of the health risks with glyphosate, both as regards it being a carcinogen and an endocrine disruptor.
"However, glyphosate's devastating impact on biodiversity should have already led to its ban. The significant public mobilisation and political opposition to re-approving glyphosate has been taken seriously by key EU governments and the Commission has been sent back with its tail between its legs."
Greenpeace EU food policy director Franziska Achterberg said: "Extending the glyphosate licence would be like smelling gas and refusing to evacuate to check for a leak. As long as there is no meaningful EU-wide restriction on glyphosate use, we will continue to live in a world that is awash in a weedkiller which is a likely cause of cancer."
"It’s scandalous, but not unusual for the Commission to keep dangerous pesticides on the market after their licences expire. It has even extended the licence for substances that Europe’s own chemicals agency has identified as highly damaging to our health. What’s new this time is that governments paid attention and didn’t just sign off on the Commission’s proposal."
Slovenian centre right MEP Alojz Peterle, president of MEPs Against Cancer, has previously voiced concerned about re-licensing glyphosate.
He said, "Given the wide use of herbicides containing glyphosate in Europe, this is an important issue for cancer prevention, not only for farmers but also for every consumer.
"The Commission should respect the Parliament's resolution on glyphosate."
Further comment came from the Health and Environment Alliance (HEAL) which has branded glyphosate as a "probable human carcinogen used in pesticides which is likely to be found every European from food, air and water."
However, speaking ahead of Monday’s meeting, the European health and food safety Commissioner Vytenis Andriukaitis insisted that the EU's authorisation procedure for pesticides is "the strictest in the world."
He said, "It takes years of scientific assessment before an active substance is authorised - or renewed at EU level. Our scientific process is very stringent and relies on pooling of expertise between the European Food Safety Authority and all member states.
"We have been aiming at a solution that commands the widest possible support of member states. So far, even though a majority of member states is in favour of the renewal, no qualified majority has been reached, in spite of the Commission's efforts to accommodate requests and concerns from a number of national governments, as well as from the European Parliament."
The Lithuanian official added, "I reiterate that for me high level of protection of human health and the environment, as provided for by the EU legislation, is paramount. At the same time, I remained deeply convinced that our decisions should remain based on science, not on political convenience. I look forward to a response from the member states."
European Crop Protection spokesperson Graeme Taylor said; "This no opinion from the committee is hugely disappointing. We share the sentiment voiced by Commissioner Andriukaitis last week when he said our decisions should remain based on science, not on political convenience.
"We frequently hear politicians proclaim Europe has the safest food safety system in the world: with this decision all they do is cast doubt on that system, and create fear and confusion amongst Europe’s consumers: the very people the system is designed to protect.
"Failure to re-approve glyphosate would have significant negative repercussions for the competitiveness of European agriculture, the environment, and the ability of farmers to produce safe and affordable food."