A bitter row has broken out over the allegedly carcinogenic qualities of a widely-used weedkiller, ahead of an EU decision on whether to continue to allow its use.

At issue is a call by the European Food and Safety Authority (EFSA) to disregard an opinion by the WHO’s International Agency for Research on Cancer (IARC) on the health effects of Glyphosate.

Glyphosate is sold and promoted by Monsanto for use with its GM crops. The herbicide makes the company $5bn (£3.5bn) a year, and is used so widely that its residues are commonly found in British bread.

But while an analysis by the IARC last year found it is probably carcinogenic to humans, EFSA decided last month that it probably was not. That paves the way for the herbicide to be relicensed by an EU working group later this year, potentially in the next few weeks.

Within days of EFSA’s announcement, 96 prominent scientists – including most of the IARC team – had fired off a letter to the EU health commissioner, Vytenis Andriukaitis, warning that the basis of EFSA’s research was “not credible because it is not supported by the evidence”.

“Accordingly, we urge you and the European commission to disregard the flawed EFSA finding”, the scientists said. Their arguments were echoed in a second open letter signed by individual health campaigners and 50 NGOs which demanded a “full and open scientific investigation“.

Commissioner condemns ‘Facebook age of science’

In a reply last month, which the Guardian has seen, Andriukaitis told the scientists that he found their diverging opinions on glyphosate “disconcerting”. But the European Parliament and EU ministers had agreed to give EFSA a pivotal role in assessing pesticide substances, he noted.

“These are legal obligations”, the commissioner said. “I am not able to accommodate your request to simply disregard the EFSA conclusion.”

A few days later, EFSA’s executive director Bernard Url hit back, complaining to the European Parliament’s environment committee that the scientists had not seen the evidence, and were leaving the domain of science by making their criticisms public.

“This is the first sign of the Facebook age of science”, he said. “You have a scientific assessment, you put it in Facebook and you count how many people like it. For us, this is no way forward. We produce a scientific opinion, we stand for it but we cannot take into account whether it will be liked or not.”

However, unease within Url’s group was growing and at the next EFSA executive meeting, board members talked candidly of a “crisis” over the issue. As well as finding the IARC’s analysis “far more credible”, the critique by the 96 scientists had appeared to snipe at EFSA’s vulnerability to influence from interest groups.

The IARC paper had relied “on open and transparent procedures by independent scientists who completed thorough conflict of interest statements and were not affiliated or financially supported in any way by the chemical manufacturing industry”, the scientists’ letter said. “It is fully referenced and depends entirely on reports published in the open, peer-reviewed biomedical literature.”

Five of EFSA’s 80 or so mammalian toxicology experts failed to file a declaration of interests, while some of those that were submitted were several years old. More than a third of the experts were also employed by national regulators and one had a 5% stake in a risk assessment consultancy.

Given the highly charged nature of the debate, EU officials privately say that the issue is most likely to be resolved in a classic Brussels-style fudge.

“The way out may be to put more limitations on certain products [containing glyphosate], or allowing member states to do that”, one EU source said. “There is a problem of the combination of glyphosate and some other substances. That is part of the reason for the difference between IARC and EFSA. But if you have additional restrictions for certain products, you give member states some leeway.”

EFSA study ‘more comprehensive’, claims chief

In a letter sent today, Url defended EFSA’s study as a “more comprehensive hazard assessment” than the IARC paper which, he said, had not tried to differentiate between the carcinogenic effects of glyphosate and other ingredients in pesticide packages, or their combined effects.

EFSA and IARC had agreed to meet early in 2016 “in an effort to clarify scientific divergences”, Url added.

However the statement will do nothing to calm the conflict. One of the scientists’ main objections is precisely that the EFSA investigation was ‘too comprehensive’, including non peer-reviewed, unpublished, industry-funded studies by scientists with grave conflicts of interest due to their industry links.

As for the scientists not having seen some of the evidence used by EFSA, one reason for that is that much of it was unpublished and IARC and other scientists do not have access to them, or can only see edited versions.

And as they stated in their letter, the IARC report “is part of a long tradition of deeply researched and highly credible reports on the carcinogenicity of hundreds of chemicals issued over the past four decades by IARC and used today by international agencies and regulatory bodies around the world as a basis for risk assessment, regulation and public health policy.”

Arthur Neslen is the Europe environment correspondent at the Guardian. He has previously worked for the BBC, the Economist, Al Jazeera, and EurActiv, where his journalism won environmental awards. He has written two books about Israeli and Palestinian identity.

This article was originally published on the Guardian Environment and is republished with thanks via the Guardian Environment Network. Some additional reporting by The Ecologist.