Climate change scientists have reacted angrily to charges that an academic paper was rejected by a peer-reviewed journal because of intolerance of dissenting views.

A paper by a group of researchers headed by Lennart Bengtsson, a University of Reading research fellow, was turned down for publication by Environmental Research Letters. Bengtsson was briefly a board member of the climate sceptic organisation the Global Warming Policy Foundation, founded by former UK chancellor of the exchequer Nigel Lawson, but he resigned on Wednesday citing pressure from other academics.

He turned to the Times newspaper to complain that the journal's rejection of his paper was on "activist" grounds. But the publishers of the journal, the Institute of Physics, said on Friday that the paper was rejected because it contained scientific flaws, and not for any political reasons.

A large number of the scientific papers submitted to peer-reviewed journals are rejected, usually because of criticisms of the scientific methods used or because the research does not represent a major new advance in thinking. Environmental Research Letters told the Guardian that it rejects about 65-70% of the papers submitted to it.

The paper in question dealt with the sensitivity of the climate to rises in greenhouse gases, claiming to have found inconsistencies in recent analyses of how much temperature is likely to rise if concentrations in the atmosphere should increase. But the reviewers found that the claim of inconsistencies was invalid, particularly as a variety of results are likely to be found by any such analysis, because all climate science deals in a range of possible future outcomes.

Nicola Gulley, editorial director at IOP Publishing, said: "The draft journal paper by Lennart Bengtsson that Environmental Research Letters declined to publish, which was the subject of this morning's front page story of The Times, contained errors, in our view did not provide a significant advancement in the field, and therefore could not be published in the journal."

She added: "The decision not to publish had absolutely nothing to do with any 'activism' on the part of the reviewers or the journal, as suggested in The Times' article; the rejection was solely based on the content of the paper not meeting the journal's high editorial standards. The referees selected to review this paper were of the highest calibre and are respected members of the international science community. The comments taken from the referee reports were taken out of context and therefore, in the interests of transparency, we have worked with the reviewers to make the full reports available."

In their reports, the reviewers stated that "the overall innovation of the manuscript is very low", and this meant it did not meet requirements for the papers in the journal to "significantly advance knowledge in the field".

They wrote: "The comparison between observation based estimates of [warming] … and model-based estimates is comparing apples and pears, as the models are calculating true global means, whereas the observations have limited coverage."

Other academics defended the peer-review process. Simon Lewis, reader in global change science at University College London, said: "What counts are the reasons the editor gave for rejection. They were because the paper contained important errors and didn't add enough that was new to warrant publication. Looking at all the comments by the reviewer they suggested how the paper might be rewritten in the future to make it a solid contribution to science. That's not suppressing a dissenting view, it's what scientists call peer review."

Joanna Haigh, co-director of the Grantham Institute on climate change, said: "This episode should not distract us from the fact that we are performing a very dangerous experiment with the Earth's climate. Even by the end of this century, on current trends we risk changes of a magnitude that are unprecedented in the last 10,000 years. How we respond to that is a matter of public policy, but scientists clearly play a key role in providing policymakers with the evidence they require."

Bengtsson said in a statement late on Friday: "I do not believe there is any systematic 'cover-up' of scientific evidence on climate change or that academics' work is being 'deliberately suppressed', as the Times front page suggests. I am worried by a wider trend that science is gradually being influenced by political views. Policy decisions need to be based on solid fact. I was concerned that the Environmental Research Letters reviewer's comments suggested his or her opinion was not objective or based on an unbiased assessment of the scientific evidence."

The paper by Bengtsson and others was submitted to Environmental Research Letters in mid-February and rejected in early March after reports by two international referees found "significant scientific errors". Following that, the authors asked for the paper to be considered as an opinion piece rather than a research paper. The journal rejected this suggestion after a further review by two other experts in the field. The final decision was made in early April.

Bengtsson was appointed to the Global Warming Policy Foundation academic advisory council on 30 April this year, and resigned barely two weeks later on 14 May. His resignation was covered by the Times the next day, with Bengtsson claiming to have been subjected to "McCarthy"-like persecution by his academic peers.

No specific examples of the persecution that took place during those two weeks were cited, and when contacted by the Guardian Bengtsson did not provide any.