Stem cell experts say they believe a small group of scientists is effectively vetoing high quality science from publication in journals.
In some cases they say it might be done to deliberately stifle research that is in competition with their own.
It has also emerged that 14 leading stem cell researchers have written an open letter to journal editors in order to highlight their dissatisfaction.
Billions of pounds of public money is spent on funding stem cell research.
The open letter to the major scientific journals claims that "papers that are scientifically flawed or comprise only modest technical increments often attract undue profile. At the same time publication of truly original findings may be delayed or rejected".
Two internationally-renowned researchers have spoken to BBC News about their concerns.
They are Robin Lovell-Badge, who is speaking in a personal capacity, and Austin Smith, from the University of Cambridge.
Professor Lovell-Badge said: "It's turning things into a clique where only papers that satisfy this select group of a few reviewers who think of themselves as very important people in the field is published.
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"You can get a lot of hype over a paper published on stem cell research that's actually a minimal advance in knowledge whereas the poor person that is doing beautiful research that is not catching the eye of the editor, you don't get to hear about that, even though it could be the world changing piece of research."
The issue is important because billions of pounds of public money are spent on funding stem cell research internationally. The funding is directed largely towards groups and individuals who have had their research published in the top journals. So if the journals are getting it wrong then public money is going to waste.
Dr Philip Campbell, the editor of Nature, which is one of the leading journals in the field, said: "Last year we used about 400 reviewers in stem cell and developmental biology, and we constantly recruit new referees. The idea that there's some privileged clique is utterly false."
It is a requirement of publicly funded research to publish in scientific journals.
This process involves sending a report of the research to an editor at a journal.
If the editor deems it sufficiently novel and interesting, they will ask two or three scientists who are experts in the field to review the research and send in comments.
It is at this stage where scientists who may well be rivals of the person who submitted their research say whether the research is good or bad. They can also suggest to the journal editor that more experiments need to be carried out in order to justify the conclusions of the research.
'Extra experiments'
The journal editor decides to publish the research paper usually when the majority of reviewers are satisfied. But professors Lovell-Badge and Smith believe that increasingly some reviewers are sending back negative comments or asking for unnecessary experiments to be carried out for spurious reasons.
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In some cases they say it is being done simply to delay or stop the publication of the research so that the reviewers or their close colleagues can be the first to have their own research published.
"It's hard to believe except you know it's happened to you that papers have been held up for months and months by reviewers asking for experiments that are not fair or relevant," Professor Smith said.
Dr Campbell denies this as far as his journals are concerned: "It's an editor's responsibility to ensure that delays are minimised, and we stop using any referee where a pattern of delays is apparent, whatever the reason might be."
These kinds of allegations are not new and not confined to stem cell research. But professors Smith and Lovell-Badge believe that the problem has become particularly acute in their field of research recently for two reasons.
Firstly, research grants and career progression are now determined almost entirely by whether a scientist gets published in a major research journal. Secondly, in stem cell science, hundreds of millions of pounds are available for research - and so there is a greater temptation for those that want the money to behave unscrupulously.
"The problem has become more common and more serious now," said Professor Smith.
"The issue here is all about public funding because you have to get these papers published to be able to get your next grant. It could be worth half a million pounds. It can be difficult for people in that position to be objective."
Even if research is not being deliberately stifled, high quality work is being overlooked as an "accidental consequence of journal editors relying too much on the word of a small number of individuals", according to Professor Lovell-Badge.
"You will have what looks like a very good paper by a very reputable scientist - but the journal takes the word of one particular reviewer too strongly. They have their favourite reviewers and what this means is that it distorts what gets published because that's going to be the view of one individual which may not reflect where the field should be going," he said.
Practical obstacles?
Dr Campbell says that as far as his journals are concerned the charge is untrue: "Our editors, who frequently attend conferences and visit laboratories in order to keep abreast of the field and the people in it, have always used their own judgement in what we publish. We have not infrequently overruled two or even three sceptical referees and published a paper."
But at a recent stem cell scientific meeting, 14 of the world's leading stem cell researchers said that journal editors hadn't seen through what they described as "unreasonable or obstructive" reviews. In an open letter to the journals, they proposed that if a paper was published, the accompanying reviews should be provided as supplementary material online.
Dr Campbell said that he was sympathetic to the idea although he envisaged practical obstacles. Professor Lovell-Badge believes that the journal editors could do more to identify bias in the review process.
"Editors should be able to see when reviewers are asking for unnecessary experiments to be carried out and if it's the difference between an opinion of the referee and a factual problem. But what tends to happen is that the editor takes the opinion of an editor rather than the factual substance," he said.
One of the main reasons for this, according to Professor Smith, is that journals are in competition. Editors have become dependent on favoured experts who both review other people's stem cell research and submit their own papers to the journal. If the editor offends these experts, they may lose future papers to a rival.
This is leading to the journals publishing mediocre science, according to Professor Lovell-Badge.
"We are seeing the publication of a lot of papers in high profile journals with minimal scientific content or advance, and this is partly because of these high-profile journals needing to keep their so called 'impact factors' as high as possible. That's determined by the number of citations that the papers have and they know that some of this trendy work is going to get cited and they seem not to care about whether its a real scientific advance or not," he said.
Commenting on the allegations, Monica Bradford, executive editor of Science, another major journal, said: "Our current policy is to preserve the confidentiality of reviewers' names and comments. Some journals have tried experiments to test the impact of open review on the quality of the feedback received through peer review.
"We have not been convinced to switch to such a system, but we will continue to monitor such experiments. We also will discuss the pros/cons of our current process internally and with our senior editorial board.
"We do recognise that human factors such as competition and potential financial gains can bias a reviewer's assessment of a paper and we expect our editors to consider these factors when evaluating the comments of the reviewers, particularly in cutting-edge areas of research."
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