Real Climate, a prominent blog run by climate scientists, may be sued by a controversial journal in response to allegations that the its peer review process is "shoddy."

Gavin Schmidt, a climate modeller and Real Climate member based at Nasa's Goddard Institute for Space Studies in New York, has claimed that Energy & Environment (E&E) has "effectively dispensed with substantive peer review for any papers that follow the editor's political line." The journal denies the claim, and, according to Schmidt, has threatened to take further action unless he retracts it.

"This is an insult, and what's more it's not true," says Sonja Boehmer-Christiansen, the editor of E&E and an emeritus reader at the University of Hull's department of geography. Every paper that is submitted to the journal is vetted by a number of experts, she said. But she did not deny that she allows her political agenda to influence which papers are published in the journal. "I'm not ashamed to say that I deliberately encourage the publication of papers that are sceptical of climate change," said Boehmer-Christiansen, who does not believe in man-made climate change.

Simon Singh, a science writer who last year won a major libel battle with the British Chiropractic Association (BCA), said: "A libel threat is potentially catastrophic. It can lead to a journalist going bankrupt or a blogger losing his house. A lot of journalists and scientists will understandably react to the threat of libel by retracting their articles, even if they are confident they are correct. So I'm delighted that Gavin Schmidt is going to stand up for what he has written." During the case with the BCA, Singh also received a libel threat in response to an article he had written about climate change, but Singh stood by what he had written and threat was not carried through.

Despite E&E's threats, Schmidt has refused to retract his comments and maintains that the majority of papers published in the journal are "dross".

"I would personally not credit any article that was published there with any useful contribution to the science," he told the Guardian. "Saying a paper was published in E&E has become akin to immediately discrediting it." He also describes the journal as a "backwater" of poorly presented and incoherent contributions that "anyone who has done any science can see are fundamentally flawed from the get-go."

As an example, Schmidt points to an E&E paper that claimed that the Sun is made of iron. "The editor sent it out for review, where it got trashed (as it should have been), and [Boehmer-Christiansen] published it anyway," he says.

The journal also published a much-maligned analysis suggesting that levels of the greenhouse gas carbon dioxide could go up and down by 100 parts per million in a year or two, prompting marine biologist Ralph Keeling at the Scripps Institute of Oceanography in La Jolla, California to write a response to the journal, in which he asked: "Is it really the intent of E&E to provide a forum for laundering pseudo-science?"

Schmidt and Keeling are not alone in their criticisms. Roger Pielke Jr, a professor of environmental studies at the University of Colorado, said he regrets publishing a paper in the journal in 2000 – one year after it was established and before he had time to realise that it was about to become a fringe platform for climate sceptics. "[E&E] has published a number of low-quality papers, and the editor's political agenda has clearly undermined the legitimacy of the outlet," Pielke says. "If I had a time machine I'd go back and submit our paper elsewhere."

Any paper published in E&E is now ignored by the broader scientific community, according to Pielke. "In some cases perhaps that is justified, but I would argue that it provided a convenient excuse to ignore our paper on that basis alone, and not on the merits of its analysis," he said. In the long run, Pielke is confident that good ideas will win out over bad ideas. "But without care to the legitimacy of our science institutions – including journals and peer review – that long run will be a little longer," he says.

According to Boehmer-Christiansen, she and Schmidt have a "long-standing" conflict that began many decades ago when he publically criticised the statistical rigour of a questionnaire she devised.

She says that she has no intention of changing the way she runs E&E – which is not listed on the ISI Journal Master list, an official list of academic journals – in response to his latest criticisms.

Schmidt is unsurprised. "You would need a new editor, new board of advisors, and a scrupulous adherence to real peer review, perhaps ... using an open review process," he said. "But this is very unlikely to happen since their entire raison d'être is political, not scientific."

• 28 February update: Bill Hughes, the publisher for E&E, on Friday reportedly told Real Climate: "...even though I am convinced you have libelled EE, please be assured I am not actually intending to do anything about."