Dr Ben Woodcock from the Centre for Ecology and Hydrology (CEH) said Bayer and Syngenta, which provided $3million in funding along with with money from Natural Environment Research Council, said he did not appreciate the companies saying he had "cherry-picked data".
He added: "We just present the results we get."
Both companies have accused the scientists of overstating the threat posed by neonicotinoids to both honey and wild bees, adding that the data, as they saw it, did not reflect the conclusions from CEH.
Syngenta argued that full results of the experiments showed neonicotinoids had no effect in the vast majority (238 of the 258) of the 258 potential effects measured.
The HTA, NFU and Crop Protection Association were among other organisations also sceptical about conclusions drawn from the study.
Woodcock told Energydesk, Greenpeace's digital journalism project.: "I’m intrigued to know what they would’ve wanted us to do. If you find negative results on key metrics – number of bees in hives, number of bees surviving after winter – how would they want us to present that? How could we interpret this in what they see as an unbiased way?
"Science papers are short. There about 1,500 words. The discussion is tiny on this. It’s like a paragraph. So it’s not like we spent vast amounts of time discussing the details of this. You literally present the results more or less as they are, along with some broad statements on what you observed."
The study examined the impact of two neonicotinoids – clothianidin (made by Bayer) and thiamethoxam (made by Syngenta) on wild bees and honey bees in three European countries: Germany, Hungary and the UK.
The experiments occurred in the field, with bees feeding on oilseed rape crops, treated with the neonicotinoids.
The results differed from country to country, with bees largely unaffected by the chemicals in Germany, which Bayer and Syngenta highlighted.
Woodcock said: "They’re trying to reduce the size of our experiment, by putting it into individual countries. And when you do that you reduce the replication to such a level that it’s basically impossible to find a difference between an effect of neonics or no neonics.
"Bayer and Syngenta said that if you look at each country individually, then you don’t get the effects you see in our study. If you do any experiment, you have to think about replication.
"Think about tossing a coin in the air: if you tossed a coin once in the air and you got heads, would you assume that you would get heads every time? No, you would do it again and again until you understand there is a 50:50 chance of the coin landing on heads. And every experiment is like that. The more times you replicate something, the more chance you have of understanding what’s going on.
"This is a problem that is well established in the literature. Previous studies have been criticised for having very poor replication because if you don’t have the replication you could report the absence of an effect of neonics even when one was present.
"They’re trying to muddy the waters. Because people aren’t aware of how the regulations work and what the regulatory body wants to focus on. They’re trying to say look at everything, rather than saying actually what they’ve presented here are the core metrics by which pesticides are regulated."
In 2013, the European Commission decided to issue a temporary ban on the pesticides in the EU, citing the risk the chemicals pose to bees.
The Commission could call for an outright ban on the chemicals at the end of 2017.
Syngenta said: "We stand by our position that this is an inconclusive study that asks more questions than it answers. It should be noted that a number of other independent scientists who have reviewed this paper expressed similar concerns via the UK Science Media Centre.
"The data generated in the study whilst variable, provides valuable and unique insights that help to better understand the ways in which neonicotinoid pesticides can be used safely. The report is a helpful contribution to the ongoing debate about pollinator health."
Woodcock added: "It’s easy to say ban neonics, but you’ve got to take into account what the alternatives are. Simply saying there’s no effect of neonicotinoids is not the way to go. There needs to be a sensible acknowledgment that there is a problem so we can work out a solution that best serves society and the natural environment."