Fourteen countries voted for the commission's proposal of a five-year extension, among them Britain, Denmark and the Netherlands.
Nine, including France, Belgium and Italy, voted against, while five abstained.
That deprived the commission of a demographic majority, since the countries voting for do not have the necessary 65 percent of the EU's population.
"France this morning maintained its position of three years and I'm proud of that," Hulot said on Thursday.
And he added that should be a plan to organise the end of the sale of glyphosate, best-known of the active ingredient of US company Monsanto's Roundup, in Europe.
Deadlock since 2016
The deadlock has dragged on since June 2016, when its previous 15-year licence expired and an 18-month extension was granted.
Opposition to the herbicide's use was boosted by a 2015 report by the World Health Organisation's (WHO) International Agency for Research on Cancer that concluded it was "probably carcinogenic".
But the European Food Safety Agency and the European Chemicals Agency say it is unlikely to cause cancer, in the light of another report by WHO experts and the UN Food and Agriculture Organisation.
Europe's main farmers' union, Copa-Cogeca, said that there is no alternative to renewal if crop yields are to be maintained.
The European Commission has said it will submit its proposal to an appeals committee.
If the stalemate continues, the licence will expire at the end of December but it will be possible to use glyphosate stockpiles for another year.
Adrian Bebb, food campaigner with Friends of the Earth Europe, Brussels, welcomed the vote.
“It shows that overwhelming public pressure is paying off and millions of people are objecting to glyphosate being used in Europe,” he told RFI. “There’s a clear lack of political support now to extend the license for glyphosate. I think this is really important because this weedkiller really locks us into industrial farming, it damages nature and it probably causes cancers.”
Friends of the Earth wants a total ban in Europe.
“If you look at papers that have been released through court cases in America, it’s clear that Monsanto, the main producer of glyphosate, has been manipulating the science over many years and when it comes to the WHO which looked at it, and looked at the independent science, they came out and very clearly saw that it probably causes cancer. That is a reason to get it off the market and help farmers to get off the chemical treadmill they’re on.”
Brexit could strengthen the anti-glysophate camp, Bebb predicts.
“The British government has always supported agro-business, supported glyphosate ... If the UK leaves Europe, as is planned, then that will actually change some of the voting patterns and one of the big cheerleaders of this industry will no longer be supporting these products in Europe.
“It’s been great that countries like France have taken a lead and really put the public safety and environmental safety at the foreground and pushing hard to get this chemical off the market.”