A Minnesota film festival is being accused of pushing a political agenda by yanking a pro-fracking documentary from its lineup while keeping two anti-fracking films on the program.

Organizers of the Frozen River Film Festival in Winona, Minn., decided last week to cut “FrackNation,” a widely discussed 2013 documentary about hydraulic fracturing, reportedly citing concerns about the film’s financial links to the oil and gas industry and the filmmakers’ inability to attend the screening.

The decision represents the first time the festival has pulled a film in its nine-year history. Instead, the festival plans to fill Sunday’s slot with a forum discussion, “Documentaries Today: My Fact Your Fiction?”

Filmmaker Phelim McAleer, who produced the “FrackNation” with Ann McIlhenney, said he wasn’t buying the festival organizers’ explanation.

“It’s a cover story,” said Mr. McAleer. “They’re under pressure from environmental elites not to show this film.”

He noted that while “FrackNation” was pulled, the festival is still showing “Gasland2,” a follow-up to the intensely anti-fracking 2011 documentary “Gasland,” and “Dear Governor Cuomo,” a documentary about anti-fracking protests in New York.

Held at Winona State University, the festival lists among its public sponsors the Minnesota State Arts Board, which donated $22,000 to this year’s event. One of the festival’s private sponsors is Winona-based Severson Oil Co., a wholesaler and distributor of oil and gas products.

Owner Tom Severson said he was disappointed in the film festival’s decision to nix “FrackNation,” and described himself as a supporter of the oil and gas industry as well as hydraulic fracturing.

“I think we should be fair about it and show both sides,” said Mr. Severson. “I’m really disappointed that something like this could happen. I’m afraid this will hurt the film festival because people will say it’s not fair, and that will hurt its credibility.”

Frozen River organizers did not respond to emails from a reporter, but an article in the Winona (Minn.) Daily News said festival officials had concerns over “whether the filmmakers have ties to the fracking industry.”

The Daily News also quoted from a Frozen River statement saying that organizers relied on the guidance of Mountainfilm in Telluride, Colo., and the Sundance Film Festival in Utah, which have not screened “FrackNation.”

“We value the advice and assistance that comes from [Mountain Film],” said the statement. “We will continue to conduct our festival with that kind of example in mind. The festival sponsors and supporters deserve nothing less than our best efforts.”

But Henry Lystad, director of Mountainfilm on Tour, said his organization had no role in Frozen River’s decision.

“After polling our entire staff, I can tell you that we know absolutely nothing about this,” Mr. Lystad said in an email. “‘FrackNation’ is not one of the films that we were supplying Frozen River this year, but regardless, we did not make any suggestions to them about not playing the film.”

The “FrackNation” filmmakers have emphasized repeatedly that they received no funding from oil and gas interests. The documentary was funded by more than $212,000 in donations collected online at the website Kickstarter, and all 3,305 individuals who donated received credit at the end of the film as executive producers.

Frozen River Chairman Mike Kennedy told the Daily News that the festival “doesn’t want to be a censor.”

“We really had to search our soul,” he said.

At the same time, he questioned the motives of the film’s supporters, saying, “Mostly local industry people who were interested in making money on the fracking business were wanting to show [‘FrackNation’].”

An email from Frozen River festival director Crystal Hegge said the film was being pulled because the filmmakers would be absent at the screening. Mr. McAleer said their attendance had never been raised previously as a condition.

“FrackNation,” described in a New York Times review as “methodically researched and provocative,” has been screened at more than a dozen film festivals in the United States and abroad.

“Basically the Frozen River Film Festival organizers have given in to bullying and taken the easy way out and censored a film that might offend environmental elites who think they know best,” Mr. McAleer said in a statement. “These people are cultural censors and don’t want the truth about fracking to be shown to audiences.”

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