"No different than if somebody has a warehouse where stolen property is being dropped off. If you created the environment that facilitated it, and you encouraged it, and you incentivised people by paying them to drop off stolen property, I think that you are complicit."
Dotcom told the programme he was targeted "because of my flamboyant lifestyle, because of me being German, the way I am".
"I'm the easiest person to sell as a villain," he said, adding: "I'm the perfect target. And that's why they picked Megaupload."
Prosecutors have rarely spoken publicly about the case, as legal wrangling about their efforts to bring Dotcom to the US for trial continues two years after his Auckland home was raided.
Mr Henry said the FBI did not file charges against Dotcom because he was a "perfect target", but because he was facilitating illegal activity.
"People sometimes tell me I look like a villain, right," Mr Henry said. "People aren't investigated because of the way they look, or the type of car they drive. They're investigated because there's an allegation that they're involved in illegal activity, that they're committing a crime."
Mr Henry also said the high-profile case against Dotcom would put other internet users off piracy.
"The FBI didn't investigate this case specifically to send a message, but certainly, that's a result," he said.
