Film-makers Debbie Melnyk and Rick Caine repeat the same mantra to anyone who presses them about their latest film and their political leanings. No, they insist, they are not rightwing, pro-Bush Republicans. If anything, they are "leftwing progressives". But perhaps the questions aren't surprising, given that in their film Manufacturing Dissent, the Toronto-based team takes on Michael Moore, the most commercially successful documentary film-maker in history, and question not only his character and work habits, but whether he has a cavalier attitude towards documentary ethics.

With Roger & Me, Bowling for Columbine and Fahrenheit 9/11, Moore has emerged as a maker of documentary blockbusters, with his features routinely taking in well over $100m (£50m) worldwide. And while challenging Moore in documentary form is not a new thing - past efforts include Michael Moore Hates America and Celsius 41.11, two anti-Moore screeds that toured the festival circuit to mixed reviews - these earlier projects were created by film-makers with a decidedly rightwing bent, and thus their attacks could easily be dismissed as ideological bile. Michael Moore Hates America, Michael Wilson's 2004 documentary feature, echoes Manufacturing Dissent, in that both films include the desperate, frustrated quest by the film-makers to get Moore to sit down for an interview. But any similarities between the other Moore refuseniks end there.

Melnyk and Caine have been making investigative documentaries for years and attest to being enthusiastic admirers of Moore's - until they decided to make a film about him. Manufacturing Dissent arrives at an intriguing moment for Moore: his new film Sicko - an attack on America's ailing healthcare system - is screening to overwhelmingly positive reviews, with even the rightwing Fox News granting it a thumbs up. But there's something sick about Moore's own fact-bending film-making techniques, at least according to Manufacturing Dissent.

The idea to profile Moore came after Melnyk and Caine made Citizen Black, a 2004 feature-length examination of Conrad Black. That film, which toured the festival circuit and was ultimately broadcast on BBC's Storyville, was filmed just as Black's fiscal fortunes began to unravel and as he was ousted as chairman of the publishing company Hollinger. "We had made a film about someone whose politics were very at odds with our own," says Melnyk, "and felt like someone closer to our outlook might be good for a change."

At first, Melnyk and Caine got some funding from a Canadian TV station and assumed their documentary would be a standard biography of Moore. They agreed with Moore's stance on the American-led invasion of Iraq and felt that he had been gutsy to make the antiwar speech he delivered at the 2003 Oscar ceremony, where he accepted the best documentary award for Bowling for Columbine. They were aware that Moore had become the personification of widespread repulsion with President George W Bush and his foreign policy, especially since Fahrenheit 9/11 - Moore's assault on the president's post-9/11 policies - which took the Palme D'Or at Cannes in 2004.

But Melnyk and Caine found themselves taking a page or two out of the Moore film-making book as they continued their research. Like the frustrated quest for an interview with General Motors' CEO Roger Smith in Moore's 1989 debut feature Roger & Me, Melnyk and Caine decided to structure their film around their efforts to get Moore to sit down and answer a number of troubling questions. Roger & Me drew critical praise for melding the personal and the political, using Moore's apparently down-to-earth persona to draw audiences in to the film's larger theme: that of corporate malfeasance and indifference. The film's central conceit was that Smith was such a heartless, appalling person, he simply would not give a frustrated Moore the time of day, let alone an interview. (The unsuccessful interview search has become a staple of Moore's films, a recurring stunt in which he and a small film crew show up at a company's headquarters, only to be told by exasperated receptionists and security staff that since they don't have an appointment, an interview will not be possible.)

Melnyk and Caine's quest becomes eerily familiar to anyone who has watched a Moore film, with security guards and even Moore's sister being fiercely protective of the film-maker. Melnyk says the research process felt a "little like losing our virginity". Suddenly, a man they had admired for years was taking on a new and sometimes unpleasant dimension. As they pursue their interview, they go over a series of charges against Moore, some about his character and work habits, others about his attitude towards documentary film ethics. The result is an occasionally disturbing portrait, though at times rather scattered. At times, former co-workers and journalists appear to suggest that Moore is egomaniacal and self- aggrandising; others make charges far more serious, contending that Moore often injects his non-fiction films with decidedly fictionalised segments.

Some of the interview subjects are former acquaintances or colleagues of Moore, who offer up negative anecdotes about the man. Not surprisingly, perhaps, the activist and former independent presidential candidate Ralph Nader is not wild about Moore - the film-maker supported Nader's 2000 presidential bid but then supported Kerry in 2004, criticising Nader for enabling Bush's victory. Nader argues that Moore is confused, a man led astray by people in Hollywood.

Some of the talking heads even suggest that Moore may have wanted two terms of Bush, given that he has now made millions by tapping into anti-Bush sentiments. If Gore or Kerry had been elected, they argue, Moore would have had far less to attack and probably would have a much diminished career.

But what is most troubling are the insinuations that Moore has fabricated things to fit his larger ideological framework. In Roger & Me, one memorable TV news clip indicated that a town hall meeting in Flint, Michigan, organised by the ABC News programme Nightline, had to be shut down after their satellite truck was stolen by an unemployed resident. The problem? "This never happened," contends Caine. "Nightline never planned a programme there, and a truck was not stolen. The clip was fabricated." If this is true, it marks a serious breach of documentary film-making principles.

If Manufacturing Dissent does come close to a smoking gun, it is in the film-makers' contention that Moore did actually get an extended interview with Roger Smith, undermining the central premise of Roger & Me. Melnyk and Caine back up their claim by including an interview with Smith, who discusses being interviewed by Moore for Roger & Me. While promoting Sicko, Moore was questioned about this claim, and said: "Anybody who says that is a fucking liar. If I'd gotten an interview with him, why wouldn't I put it in the film? Any exchange with Roger Smith would have been valuable." Moore goes on to say that the interview he got with Smith took place years before he made the film and that his fruitless efforts to get another interview with Smith as depicted in the final cut are genuine. But Caine and Melnyk stand by their assertions, providing evidence in print and in testimonials that contend that Moore spoke with Smith during the period he claims he could not get an interview with the CEO. Moore did not return requests from the Guardian for an interview about his response to Manufacturing Dissent.

Even if Caine and Melnyk's worst-case assessments of Moore are true, there are some who would argue that they should still leave the man alone. They point out that Moore has been an important critic of Bush and the Iraq war, during a period when the American media seemed to cower at offering any real and thorough counterpoint to the Bush administration and its policies. Indeed, many now argue that the lead-up to the invasion of Iraq is as much about the failure of American journalists to do their jobs as it is about sabre-rattling on the part of the military, and that Moore emerged as one of the rare, valiant voices of dissent. In other words, if a few facts get trodden on or overlooked, Moore's hyperbolic style should be forgiven, as he is pointing to crucial truths.

"I disagree completely," says Caine. "Documentary film-makers and journalists must operate on a basic premise: we should expose lies, not make them. By distorting things, Moore is actually hurting the left and handing the right a huge club to wield. Once people see that he's distorted so many things, it allows them to dismiss the entire argument." Melnyk and Caine are backed up by respected documentary film-makers in Manufacturing Dissent, including Albert Maysles (Gimme Shelter, Grey Gardens) and Errol Morris (The Fog of War), both of whom express their reservations about Moore's tactics. Maysles even goes so far as to suggest that Moore might actually hate America.

And while Melnyk and Caine don't manage to get a lengthy, sit-down interview with Moore, they do meet up with him at one point. Melnyk asks Moore if there might be a point when they could conduct a longer interview; Moore responds that he is too busy on his current publicity tour - which seems a believable answer. The meeting effectively keeps the Moore mystique alive. He praises Melnyk for being Canadian, and then offers her a hug, one that is executed uncomfortably before his handlers shuffle him along. Given Melnyk and Caine's filmography, it prompts an obligatory question: who was easier to deal with as a subject, Black or Moore? "Actually, Conrad Black was really quite gracious and polite. He was much easier to deal with than Michael Moore."

Manufacturing Dissent screens tonight and tomorrow at the Edinburgh film festival. It is released on DVD in October.