The show, set to air on Tuesday, focuses on a ‘legal grey area’ called Chako Ero which sees kids forced to wear sexy costumes because of an obsession with “virginity”.
Dooley spoke to one producer, who admitted he had filmed a six-year-old girl playing with toys while she was dressed in a swimming costume.
“We filmed her playing in her bathing costume, playing with the toys,” he told the show.
“Her mum was standing behind the camera with her favourite doll. There are lots of guys in Japan who have this Lolita complex.
“The younger they are, the more likely they are to look like virgins.”
Possessing child pornography was only made illegal in Japan three years ago.
But despite the stricter rules, the investigation found that sexual images of young girls are still being “openly and widely distributed" for commercial gain.
Chako Ero exploits a legal loophole because the children wear clothes - usually sexual costumes - in the photoshoots.
“Japan is seen to have a serious problem with the sexualisation of children,” a BBC spokesman said.
Dooley also visited a legal Tokyo JK café where schoolgirls are paid to hold hands and talk about sex with older men.
She spoke to police in Japan who say they are doing their utmost to protect vulnerable girls.
The filmmaker was held by Japanese police for two hours after the crew shot footage of two schoolgirls walking on a Tokyo street where men can rent teenagers.
In footage of the incident, two men can be heard telling the presenter “no movies" and demanding the crew erase footage.
Stacey Dooley Investigates Young Sex for Sale in Japan will be available to watch on BBC Three from 10am on Tuesday.
You can watch a disturbing 4 minute excerpt from the documentary here.