The veteran director has come under attack in recent days from several Hollywood stars who accuse him and Marlon Brando of abusing actress Maria Schneider by keeping her in the dark about how the scene was to be shot.
Bertolucci, 76, acknowledged Schneider was not aware that Brando's character would use butter as a lubricant during the scene in which the actor simulates anally penetrating his lover, played by then 19-year-old Schneider.
"I want for the very last time to clear up a ridiculous misunderstanding," Bertolucci said in a statement about the steamy 1972 movie.
"We wanted her spontaneous reaction to this improper use (of the butter). The misunderstanding arises from this. People thought, and think, that Maria was not informed of the violence she was to suffer (in the scene). False!
"Maria knew everything because she had read the script, in which it was all described."
Bertolucci spoke out after the recent resurfacing online of a 2013 interview in which he said he and Brando had decided to introduce the butter without informing the actress.
Bertolucci, considered one of the giants of Italian and world cinema, confirmed that was what happened.
"The only new thing was the idea of the butter. It was this, I learned many years later, that upset Maria, and not the violence that was in the scene and was envisaged in the script of the film.
"It is both consoling and distressing that anyone could be so naive to believe that what happens on the cinema screen actually takes place.
"Those who do not realize that sex is (almost) always simulated in films probably believe that every time John Wayne shoots an enemy on film that someone really dies."
Schneider, who suffered drug addiction and depression before her 2011 death, said four years earlier she had felt "a little raped" during the scene and was profoundly angry about it for years afterwards.
The relaying of Bertolucci's interview comments have prompted outrage on social media, fuelled by top actors.
"To all the people that love this film - you're watching a 19yr old get raped by a 48yr old man. The director planned her attack. I feel sick," Oscar-nominated Jessica Chastain wrote on Twitter.
In the 2013 exchange, Bertolucci explains how the butter idea came about. "We were having, with Marlon, breakfast on the floor of the flat where I was shooting," the director says.
"There was a baguette, there was butter and we looked at each other and, without saying anything, we knew what we wanted."
Actor Chris Evans said on Twitter: "I will never look at this film, Bertolucci or Brando the same way again. This is beyond disgusting. I feel rage."
"Westworld" star Evan Rachel Wood, who recently opened up about her own sexual abuse, described Bertolucci and Brando - who died aged 80 in 2004 - as "very sick individuals to think that was ok."
By Angus MacKinnon