Technicians were shooting footage of an explosion for the pounds 40m version of the television series when it went out of control. Sixty firefighters were called in to tackle the blaze in a scene that could almost have been straight out of the film.
The opening scenes of the film, which stars Uma Thurman as Emma Peel and Ralph Fiennes as John Steed, were shot this week. Neither of the stars were on stage at the time.
The film's producer, Jerry Weintraub, said it was too early to assess the extent of the damage to the set and whether it would delay production of the Warner Brothers film, which was due to be completed in September.
"It's a serious blow, but as long as nobody dies or gets severely injured, then we'll get over it," he said. "The Avengers always deal with everything."
The fire at the studios in Buckinghamshire broke out at around 5pm in Stage E, which is used as a sound studio.
In total, 60 firefighters were called to the scene. A member of the studios' own firefighting team was taken to hospital suffering from smoke inhalation.
The fire started in a roof space between insulation and roofing panels. As one witness explained: "Some sparks for the explosion shot up 30 feet and set light to the roof."
A spokesman for Buckinghamshire Fire Brigade said that firemen had to cut away the insulation in the roof to get to the seat of the blaze.
The spokesman added that an investigation was under way into how the controlled explosion went wrong. He added: "We are also looking into why the studio failed to tell us that they were having a controlled explosion today.
"Usually, whenever explosions are being carried out, they inform us but this time they didn't."
Fire crews were expected to remain at the studios throughout the night - although the blaze was well under control.
Pinewood has been at the forefront of the 1990s improvement in fortunes for British film-making. Successes at the country's biggest studio have included Mission Impossible, Interview with the Vampire and The Saint, in a turnround from the staff-cutting days of the 1980s.
Over 60 years, the Buckinghamshire studio's success has been the result of an unlikely partnership between James Bond, the Carry On team and Superman. It was also the place where Laurence Olivier kissed Marilyn Monroe in The Prince and the Showgirl and where David Lean made Great Expectations.
The studio was built in the 1930s by a film-struck builder, Charles Boot, and the millionaire J Arthur Rank. The studio set the standards for film production in this country. But the late 1980s and early 1990s were grim with high exchange rates discouraging American film makers to bring their productions to Britain.Reuse content