The International Assessment of Agricultural Science and Technology for Development aims to focus attention on the problem of how to feed the world's growing population, as the Intergovernmental Panel on Climate Change has done for the challenge of global warming. Monsanto, Syngenta and BASF resigned after a draft report from the project highlighted the risks of GM crops and said they could pose problems for the developing world.
The companies argue the report should say their GM technology could secure future food supplies because it can boost yields and make plants more resistant to droughts and higher temperatures.
Bob Watson, director of the project, which is based on the work of 4,000 scientists and experts from around the world, said he was "very disappointed" by the companies' move.
He said: "It's very unfortunate that they have walked out even before we agreed the final version. If they can bring evidence forward that we have not been objective, or that the language is biased, then we could discuss that."
He also said the resignations would weaken the final report. "Our goal was to have them included. We wanted a multi-stakeholder group that included everyone, that was absolutely essential."
The project was due to agree its final report last week in Nairobi, but the meeting was postponed because of the unrest in Kenya. It is now expected to finish in April.
Croplife International, the agriculture industry trade body of which Monsanto, Syngenta and BASF are members, told the project's leaders it was unhappy that the views of its members had not been reflected in the draft report, and that they were pulling out.
Denise Dewar of Croplife International said: "We were concerned with the direction the draft was taking and that our input was not being taken appropriately. We were looking to see references to plant science technology and the potential role it can contribute."
The draft report says there is a "wide range of perspectives on the environmental, human health and economic risks and benefits of modern biotechnology, many of which are as yet unknown". It says it is not clear whether GM crops increase yields and warns that use of the technology in the developing world could concentrate "ownership of agricultural resources" in the hands of the companies involved, as well as causing problems with patents.
In an editorial criticising Croplife International's decision, the science journal Nature said: "The views outlined in the draft chapter on biotechnology, although undoubtedly over-cautious and unbalanced, do not represent the rantings of a fringe minority. The idea that biotechnology cannot by itself reduce hunger and poverty is mainstream opinion among agricultural scientists and policy-makers."
Greenpeace, a member of the assessment project, urged the companies to reconsider. Jan van Aken, GM campaigner with Greenpeace International, said: "This assessment goes far beyond genetic engineering, it is about setting solutions for global agriculture and the world's poor and hungry. It is such a shame to withdraw from such a good initiative, simply because your business plans do not fit with sound science and experts voiced a more balanced opinion than yours."