In fact, they believe that in some cases the process "risks turning into unsolicited authoritative advertising for the drug industry". But what does their argument mean? And what do researchers see as the best possible solution?
A team led by Tom Jefferson, from the Italian-based group, wrote in the British Medical Journal (BMJ) recently that, "scientists need access to all unpublished data, even of trials published in the peer-reviewed literature".
"It is time the media, the Cochrane Collaboration and any reader interested in knowing what they are prescribing or are being prescribed increase the pressure on policy makers. If you swallow a medication, you need to know how it works – for real," they asserted.
The Cochrane team's arguments are based on an already-contentious issue illustrated by an updated systematic review of Roche's Tamiflu drug, the anti-viral medicine oseltamivir, published in the BMJ just over a year ago.
Some industry groups questioned whether publicly-available data on the drug was adequate to support any conclusions about its efficacy in reducing the risk of complications, such as pneumonia, in otherwise healthy flu patients.
At the time, Roche gave a highly-detailed rebuttal of the Cochrane researchers' conclusions in a letter to the BMJ, which claimed that it was not standard practice for study protocols or reports to be made public.
The firm also questioned on that occasion why requests for additional data on Tamiflu had come from the broadcaster Channel 4's news desk, rather than from the researchers themselves.
Revisiting the debate over whether the motives behind inquiries were "truly for clarity and scientific validation", the latest BMJ article from Mr Jefferson and his team notes Roche's public pledge to make full clinical study reports on the drug available.
They added: "We expected that these reports would provide sufficient detail to verify the findings of the Kaiser meta-analysis," referring to the 2009 review's exclusion of findings from unpublished trial data incorporated into Tamiflu trials led by Laurent Kaiser. Only two of these actually appeared in the peer-reviewed literature.
Jefferson's team continued: "What Roche provided was not the full study reports of the ten trials but module one of seven trial reports. The tables of contents showed that the full reports probably comprise four or five modules.
"Unfortunately, module one does not include the analysis plan, randomisation schedule details, the study protocol with a list of deviations, or detailed case histories for patients experiencing adverse events."
They argued that, though incomplete, the extra data provided were another reason for questioning the credibility of evidence published.
"For example, the first of the two published studies in the Kaiser meta-analysis does not mention serious adverse events and the second states that 'there were no drug-related serious adverse events'.
"However, the partial study reports that Roche made available to us list ten serious adverse events in the two trials, three of which were classified as possibly related to [the drug]."
As a possible solution to the issues they contend, Mr Jefferson and his Cochrane team suggested that industry officials needed to take control of the situation, making all data publicly accessible.
"Ideally, regulators would make full clinical study reports publicly available once a regulatory decision is reached," they wrote, though the scientists admitted this represents "a daunting task considering that the FDA submission for oseltamivir was at least 363 volumes".
In the mean time, the researchers called on journals to demand "submission of the most-detailed report available, in addition to the summary manuscript for publication", when deciding whether to publish details of a randomised trial.
They added that an overview of the study programme should also be submitted, explaining the reasoning behind – and findings from - each individual trial.
"We need to understand how and why a particular trial was designed and conducted – that is, how every trial can potentially advance our knowledge."