Pesticide maker Syngenta has withdrawn an “emergency” application to use a banned insecticide on up to a third of all oilseed rape in the UK. The U-turn follows a major outcry from green campaigners but the company blamed the government for failing to make a decision in time for crop sowing.

Syngenta’s neonicotinoid pesticide was given a two-year ban by the European Union in 2013 due to research linking it to serious harm in bees. Neonicotinoids are the world’s most widely used insecticide and in June an international scientific review concluded that contamination was so pervasive it threatened global food production.

Syngenta argued that there was a future pest threat to oil seed crops that justified an emergency exemption and the government’s advisory committee on pesticides said the criteria for an exemption had been met, although the evidence of the threat was not made public.

“Following an assessment of the current planting schedule for growers, Syngenta has decided to withdraw its application,” said a company spokesman. “Syngenta was clear that in order to supply the product to British farmers and, importantly, to ensure its effective stewardship, an approval from government was required by the end of June.” The spokesman said the company was considering re-applying in 2015.

Guy Smith, vice president of the National Farmers Union, said: “It is very frustrating that it was not possible for a decision to be made in time for Syngenta to prepare seeds for this year’s planting. This loss of this treatment will make it more complicated to grow oilseed rape this season.” He said the issue had been “heavily politicised” by campaign groups with their “own agenda against pesticide use”.

A spokesman for the Department of Environment, Food and Rural Affairs said: “This was a complex application that had to be considered according to EU rules.”

Over 200,000 people protested against Syngenta’s application via the 38 Degrees campaign site, while 35,000 wrote to environment secretary Owen Paterson via Avaaz and another 6,000 Friends of the Earth supporters asked ministers to “stand firm against Syngenta”.

“Our under-threat bees can breathe a bit easier,” said Andrew Pendleton, from Friends of the Earth. “We’re delighted Syngenta has withdrawn this application. The scientific evidence linking neonicotinoid pesticides to bee decline is stacking up. Ministers are currently finalising their action plan for protecting Britain’s bees and it must get tough on all the causes of bee decline, including pesticides.”

Bert Wander, Avaaz campaigner, said: “It’s great news that the huge swarm of protest killed off Syngenta’s attempts to try and keep their bee-killing poisons in Britain’s fields. We welcome their withdrawal and we hope this is the end of it.”

Shadow environment minister Barry Gardiner also welcomed the withdrawal of the application: “It would have driven a coach and horses through the temporary ban put in place to gather scientific evidence. But we need a serious pollinator strategy from government: neonicotinoids are not the only problem.”