Miller called the Occupy protestors "thieves" and "rapists" in a controversial blog post. His remarks attracted widespread criticism across the entertainment industry.
Moore has now described the movement as "a completely justified howl of moral outrage", and distanced himself from Miller's views on the subject.
"I think that the Occupy movement is, in one sense, the public saying that they should be the ones to decide who's too big to fail," the Watchmen writer told Honest Publishing.
"It's a completely justified howl of moral outrage and it seems to be handled in a very intelligent, non-violent way, which is probably another reason why Frank Miller would be less than pleased with it.
"I'm sure if it had been a bunch of young, sociopathic vigilantes with Batman make-up on their faces, he'd be more in favour of it. We would definitely have to agree to differ on that one."
Moore previously commented on the protestor's use of the Guy Fawkes masks popularised by his V for Vendetta graphic novel, saying that the story's protagonist has "escaped the realm of fiction".
MTV plans to air a documentary on the Occupy protests as part of its True Life series.