Fiona Godlee told the second hearing of the Commons Science and Technology Committee's peer-review inquiry that journals were "largely naive" about the "extremely dubious" practices of the pharmaceutical industry.
"For every good reason, and lots of bad reasons, (companies) want to get their results out into the public domain, and journals provide them with a very effective way of doing that," she said. "It has been said that journals are the marketing arm of the pharmaceutical industry, and that is to a large extent true."
Dr Godlee said publishers also needed to do more to acknowledge that the pharmaceutical industry was a major source of their income.
Claiming that editorial decisions in medical journals were often "directly influenced" by the revenue generated from sales of reprints of articles to pharmaceutical companies, she called on the committee to investigate the issue.
"I defy any editor presented with a very large drug trial not to know when they are accepting it that it will generate revenue for their journal," she said. "Publishers benefit, but I don't think science benefits."
She called for the establishment of a central system for declaring conflicts of interest, and said publishers also needed to do more to make it clear when journals they published were sponsored by pharmaceutical companies and did not carry out traditional peer review.
In 2009, Elsevier admitted that it had published several journals that it had not acknowledged were sponsored. Dr Godlee also described peer review as "extremely limited" because journals were "reliant on what authors send us", and she called for the full submission of data by authors to be made mandatory.
She added that, given its importance to science, peer review was "remarkably undervalued" and under-researched, and she called on journals, funders, industry and the government to fund more research.