A study on which the UK government bases its position that neonicotinoid pesticides do not threaten bees may actually be the first conclusive evidence that they do, according to a leading bee scientist.

Dave Goulson, a professor of biology at the University of Sussex, reanalysed a 2013 study on the effect of the world’s most heavily used pesticides on bumblebees by the UK’s Food and Environment Research Agency (Fera).

Fera’s scientists said that bee hives “remained viable and productive in the presence of the neonicotinoid pesticides under these field conditions”. Yet, Goulson said the experiment found that all hives where clothianidin, a common neonicotinoid, was present had reduced numbers of queen bees.

Goulson said: “The conclusions they come to seem to be completely contrary to their own results section.”

“They find that 100% of the time there is a negative relationship between how much pesticides were found in the nest and how well the nest performed, and they go on to conclude that the study shows that there isn’t a significant effect of pesticides on bee colonies. It doesn’t add up.”

The study was never published in a peer-reviewed journal and has been rejected by the EU’s safety authority. Yet the Department of Environment, Food and Rural Affairs (Defra) cites it on their website as a foundation for its support of the pesticides.

A Fera spokesman appeared to agree that the government has drawn the wrong conclusion from the study.

“In the executive summary of our 2013 report we clearly stated that our experiment lacked the power to reach any firm conclusions about the impact of seed coated neonicotinoid on bumblebee health. Whilst there was an absence of evidence to support the hypothesis that neonicotinoids harm bees, this does not lead to the conclusion that they are benign,” he said.

A Defra spokeswoman said the new analysis would be reviewed by the independent advisory committee on pesticides to ensure their policy was “based on the best scientific evidence available”.

Recent studies have shown that neonicotinoids damage the health of bee hives. But they have been criticised for not being conducted in the field. Field experiments are notoriously difficult because of the roving behaviour of bees and the massive amount of neonicotinoids already pervading the environment.

Goulson said the Fera experiment, in which controlled hives became contaminated with pesticides, was flawed. After their original design failed, the Fera scientists used a complicated statistical analysis to assess whether there was a correlation between the amount of neonicotinoids present in a hive and the number of queens produced.

Goulson said the approach was “peculiar” but “acceptable”. However the scientists had drawn the wrong inferences from their data.

“Despite the conclusions originally drawn by Fera, their data appear to provide the first clear evidence that colonies of free-flying bumblebees exposed to neonicotinoids used as part of normal farming practice suffer significant impacts in terms of reduced colony growth and queen production,” said Goulson in his report.

Flaws in the experimental method of the Fera scientists have previously been pointed out by the European Food Safety Authority (Efsa). The findings of the study were discounted by Efsa when making its 2013 recommendation to the EU that neonicotinoids posed an “unacceptable” risk to bee health.

The lead author on the Fera report left the agency just months after its publication to work for Syngenta – a major producer of neonicotinoids. This lead to suggestions that the government was too close to the pesticide industry.

The former environment secretary, Owen Paterson, relied heavily on the research to make his case against the EU moratorium on neonicotinoids. The ban was introduced in 2013, despite the UK lobbying, and eventually voting, against it. The legislation will be reviewed in December.

Matt Shardlow chief executive of the invertebrate charity Buglife said: “Owen Paterson justified the UK’s pro-neonicotinoid position using the Fera bumblebee field study. However concerns about its ‘elaboration and interpretation’ of results were soon raised by an EU scientific body. The new reanalysis of the study reverses the interpretation, it now clearly shows that neonicotinoid polluted bumblebees produce fewer queens, and calls into question Defra’s scientific integrity.”

Goulson said if the Fera report had been subject to the normal scientific process of peer review then it may have been discredited earlier. He said government should reconsider basing policy on non-reviewed reports.

“It is ... concerning that the same data set can be interpreted in such wildly contrasting ways by different scientists, for this is likely to undermine confidence amongst the general public in the scientific process.”