Megumi Igarashi, 42, had allegedly displayed an “obscene” work at a Tokyo sex shop and sent 3D data of her genitals to other people.
She was arrested in early December and has been held in detention since then.
Ms Igarashi was previously arrested in July, but was later released following a legal appeal and public pressure.
On Wednesday Ms Igarashi was charged with obscenity for displaying a work modelled on her vagina and for distributing data that could be used to print out a 3D copy of her genitals, reported the Asahi Shimbun newspaper.
Ms Igarashi, who goes by the name Rokudenashi-ko which means “no-good girl” in Japanese, pleaded not guilty.
Asahi Shimbun reported that she read out in court a prepared statement which said: “My works are all meant to induce friendly laughter because they involve cutely decorating sexual organs. The works are not obscene.”
Japan’s obscenity laws ban the depiction of genitalia, which are blurred in broadcast media and images.
If convicted, Ms Igarashi could be jailed up to two years and/or fined as much as 2.5 million yen (£13,350, $20,750).
Ms Igarashi made international headlines in July when she was arrested, after she raised funds online to make a vagina-shaped kayak using a 3D printer.
She had sent data that could be used to create 3D models of her vagina to those who had donated to her.
She was released after several days following a legal appeal and a petition signed by more than 17,000 people saying her work was art and not obscene, reported Japan Times.
But police arrested her again on 3 December on similar grounds.
They also arrested the owner of a Tokyo sex shop for allegedly displaying Ms Igarashi’s “obscene goods” in her shop window from October 2013 until July this year. The woman was later freed after a judge refused to allow prosecutors to question her further.
Authorities however were allowed to continue to detain Ms Igarashi because the judge was concerned that she would “destroy evidence or flee”, said Asahi Shimbun.
Her case has sparked debate on the nature of censorship and Japan’s obscenity laws.
Correspondents say that opinion is split in Japan over whether Ms Igarashi’s work is obscene, with some pointing out that images of penises are not seen as causing offence.
On her website, Ms Igarashi, who has made several items based on her genitals using a silicone mould, said she wanted to make vaginas “more casual and pop”, much like how penises are regarded as “part of pop culture” in Japan.