The EU has been criticised after a new legal analysis showed it had allowed scores of “emergency authorisations” of banned pesticides that threaten bee colonies.

The research emerged as the EU’s general court began hearing a case by Syngenta and Bayer to overturn the pesticides ban. A ruling is expected shortly.

Three neonicotinoid pesticides were outlawed in Europe in 2013, following analysis – since confirmed by the pesticide industry’s own research – that they posed a grave risk to bee populations.

“Limited and controlled” exceptions to the ban were permitted for emergencies, where pest outbreaks posed an imminent economic danger that could not be treated any other way.

In those conditions, countries could notify Brussels that they were exercising a derogation and provide their justifications for scrutiny. In practice though, that scrutiny was lacking, according to ClientEarth.

Vito Buonsante, a co-author of the new research for ClientEarth, said: “The [European] commission has been utterly complacent and done nothing to limit this clear abuse of the law. Instead of scrutinising the actions of member states as they are obliged to do, they have closed their eyes and continued with business as usual. It is negligent.”

The group’s analysis finds that 82% of country notifications did not provide any economic evidence of a threat to plant production, and around the same percentage did not list any alternative means of pest control.

A requirement to identify the infested area was breached in 62% of cases and most countries provided no evidence that the neonicotinoids would be used in a limited and controlled way.

Most worrying for environmentalists, while the exemptions were intended to help farmers facing sudden infestations, and states protecting ecosystems from exotic pests, 44% of requests for derogations were filed solely by pesticides manufacturers, trade associations or seed producers. Only 14% were filed without any industry involvement.

Dominique Doyle, another of the report’s co-authors, said: “Our interpretation is that the derogations requested solely by industry are not in line with the aims of the directive and are illegal – all 44% of them. They should have been refused by the commission.”

Romania was the leading EU applicant for derogations, with 20 notifications, closely followed by Finland and Estonia, with nine each. The UK notified Brussels of three emergency authorisations.

The European commission could not confirm the findings of the ClientEarth’s report, but said that derogations were primarily the responsibility of notifying countries.

A spokesperson told the Guardian: “In line with the EU legislation on sustainable use of pesticides, all member states need to reduce the use of all plant protection products both in general terms and in sensitive areas such as parks and gardens, sports and recreation grounds, school grounds and children’s playgrounds, and in the close vicinity of healthcare facilities.”

• This article was amended on 17 February 2017 to add a quote from the European commission that was received after the article was first published, and to correct the number of Estonian derogations and the name of the court hearing the Syngenta/Bayer case.