Two of the world’s most widely used insecticides cause significant harm to bumblebee colonies, a new study has found, but a third had no effect.

The work shows the distinct effects of each type of neonicotinoid pesticide, from cuts in live bees and eggs to changed sex ratios and numbers of queens. Previously, the different types of neonicotinoids have often been treated as interchangeable.

Neonicotinoids and other pesticides have been implicated in the worldwide decline in pollinators, which are vital for many food crops, although disease and loss of habitat are also important factors. There is strong evidence that neonicotinoids harm individual bees but little evidence so far that colonies suffer as a result. The EU imposed a moratorium on the use of neonicotinoids on flowering crops in 2013.

The new study examined the effect of three neonicotinoids from the level of brain cells to colonies in the field. The latter involved 75 colonies across five sites in Scotland and included control colonies that were not given access to the pesticides.

The research found that both imidacloprid (made by Bayer) and thiamethoxam (Syngenta) at realistic levels of exposure harmed the bumblebee colonies. For example, imidacloprid cut the number of brood cells, which contain eggs, by 46%, while thiamethoxam reduced the number of live bees by 38%. But clothianidin (Bayer) had no effect other than increasing the number of queens produced.

“There is clear evidence that imidacloprid and thiamethoxam are harmful to bees but our evidence raises a question over clothianidin,” said Dr Christopher Connolly, at the University of Dundee and who led the research published in the peer-reviewed journal Science Reports.

“I think there is sufficient evidence for a ban on imidacloprid and thiamethoxam, but not for clothianidin although the moratorium should continue,” as more evidence is gathered.

A study published in November found that honeybee colonies exposed to thiamethoxam were able to compensate for bee deaths by producing more workers, so no overall impact was seen. However, honeybee colonies have far more individual bees than bumblebees, suggesting the latter have far less ability to compensate.

The only effect seen in the new study from clothianidin exposure was an increase in queens. “The number went through the roof,” said Connolly. “The purpose of a colony is to produce queens so this could be a really good thing, unless, say, all those queens turn out to be infertile.”

Connolly said the research did not show clothianidin was harmless to all pollinators: “It does not show it is safe, but it does show it may be less harmful to bumblebees.” He said the work showed the effects of one neonicotinoid could not be assessed from studies on another: “All three behave completely differently. You can’t predict the insect-insecticide relationship by extrapolation.”

“This is an important and timely study,” said Mike Garratt, an ecologist at the University of Reading and not involved in the new research.

“As the body of evidence for negative effects of neonicotinoids on non-target species mounts, it is important to consider the differential effects of these chemicals. This study only considers impacts on one species of bumblebee. Similar variability in toxicity might be expected for other species of bee and non-target organisms, and it is important to remember there are more than 200 distinct bee species in the UK alone.”

Prof David Goulson, a bee researcher at the University of Sussex and also not involved in the new research, said: “The [new information on variable effects] makes assessing the impacts of these chemicals even more challenging [and], even more confusingly, bees are often exposed to a mixture of several neonics, the effects of which we haven’t begun to understand.”

But spokesmen from the pesticide manufacturers challenged the research. “The apparent colony effects reported in this study for thiamethoxam contradict a previous study, which reported no adverse effects on bumblebee micro-colonies,” said Peter Campbell, from Syngenta. “This study struggles to explain the inconsistent results found across the [brain cell], laboratory and colony experiments, which often contradicted each other as well other previous published data.”

Julian Little, from Bayer, said: “This paper continues a narrative where different research groups find different, and in many cases, no impacts of insecticides on different bee species. It underlines the importance of not making kneejerk reactions in response to individual papers.”

Connolly criticised EU regulations that allow pesticide manufacturers to conduct the safety trials themselves. “It is ludicrous to have industry doing their own testing and then keeping the results as proprietary information.”

Neonicotinoids have been used for two decades, but Connolly said: “It has taken years and millions of pounds for scientists to wave a red flag.”

In a separate development, the UK’s National Farmers Union (NFU) has applied for an “emergency” lifting of the moratorium for some oilseed rape to deal with a pest beetle, but campaigners say rape yields have actually increased since the neonicotinoid ban.

NFU vice-president Guy Smith said this week: “After assessing the evidence and having listened to the experiences of our oilseed rape growing members this autumn, the NFU has applied for emergency use of neonicotinoid seed treatments on a limited proportion of the oilseed rape crop in England.”

The NFU was granted a suspension of the ban for about 5% of rape fields in 2015, a move opposed by a 500,000-strong petition.

Friends of the Earth’s Dave Timms said: “Allowing farmers to use banned bee-harming pesticides would be reckless and unnecessary. Oilseed rape yields have actually risen since the pesticide ban was introduced, while the evidence of the harm these chemicals pose to bees has increased.”