A widely used insect nerve agent that harms bees will be banned from use on corn and sunflowers in Europe from the end of 2013, after member states overwhelmingly backed the proposal in a vote on Tuesday. However, the UK once again failed to back measures to restrict pesticide use.

Fipronil is used in more than 70 countries and on more than 100 different crops, but in May the European Food Safety Authority labelled it a "high acute risk" to honeybees. A similar assessment by the EFSA on three other neonicotinoid insecticides, based on increasing scientific evidence of harm, also preceded the suspension of their use in the European Union in April.

Tonio Borg, European commissioner for health said: "In the aftermath of the restriction on use of neonicotinoids, I pledged to do my utmost to protect Europe's honey bee population and today's agreement with member states, not only delivers on that pledge but marks another significant step in realising the commission's overall strategy to tackling Europe's bee decline."

Bees and other pollinators are essential in the growing of three-quarters of the world's crops, but have seen serious declines in recent decades due to habitat loss, disease and pesticide use. In Tuesday's vote, only the UK, Slovakia and the Czech Republic abstained and only Spain – the biggest user of fipronil – and Romania voted against. The UK was also one of eight of the 27 EU member states that unsuccessfully opposed the EC neonicotinoid ban.

"The UK abstained from the vote as there were concerns that the proposals were not based on sound scientific evidence," said a Defra spokeswoman. "Fipronil is not used in any authorised pesticide in the UK so this ruling will have little impact [here]."

Paul de Zylva, of Friends of the Earth, welcomed the "leadership" of the European commission but added: "Yet again the UK's pesticide testing regime has proven to be unfit for purpose. It's disappointing to see the UK government abstaining from another cut and dried opportunity to protect bees."

In June, the UK government launched an "urgent" review of the crisis facing bees and other pollinators in the UK and pledged to introduce a national pollinator strategy. De Zylva said: ''The UK government must now prove its commitment to reversing bee decline. Ministers must deliver a strong national pollinator strategy by November and respond to MPs' calls for an overhaul of the nation's system for testing pesticides."

Fipronil, which is also used for cockroach and termite control, is manufactured by the German chemical company BASF. "Sound data from field studies that underpin the safe use of our product for bees were not considered sufficiently," said Jürgen Oldeweme, at BASF Crop Protection. "We are certain that Europe can achieve both – the protection of pollinators and the support of European agriculture – but for that all stakeholders must engage in a comprehensive action plan to address the real root causes of the decline in bee health."