The GLADIATOR star was playing a scene in which Cash recalled the death of his older brother Jack, who died in a horrific wood-saw accident aged 14.
Phoenix's brother RIVER died of a drug overdose in 1993 outside Los Angeles nightclub The Viper Room
The 30-year-old actor reportedly broke down and repeatedly banging his head into a bedpost during the filming and was taken away in an ambulance.
But Phoenix denies reports he was affected by the scene, and insists he was just getting into the mood of his character - a young Johnny Cash going through drug withdrawal.
Phoenix tells the New York Daily News, "That's not the way my brain works.
"You know, the press has kind of imposed upon me the title of 'Mourning Brother', and because I haven't been vocal about it, the assumption is that I'm holding on to it and all this s**t that's just not there.
"I don't need to pull from my experience for a character, and I've never understood why actors would, except for lack of ability, imagination or research.
"I had all three things, so this is a little frustrating to me, because it denies my work and the research that I did."
The biopic movie - in which PHOENIX stars alongside REESE WITHERSPOON - is due to hit screens this November (05).