Standing on a wall in front of the railings outside the courthouse, the women, two French and the other German, shouted: "Free Amina," in support of a young Tunisian woman detained while protesting against hardline Islamists and awaiting trial on Thursday.
"Breast Feed Revolution" read graffiti on the women, who wore only denim micro shorts and black shoes, and "Femen Extremist" was daubed on their backs.
The police swiftly arrested them and took them inside the building, before a crowd of journalists.
The Femen protest, also intended to highlight the difficulties facing women in socially conservative Tunisia, provoked the anger of onlookers, some of whom tried to cover up the women.
A group of lawyers linked to the hostile crowd attacked some of the journalists, accusing them of giving a platform to the topless activists.
As the young women were being transferred from one office to another within the court building, the lawyers sang the Tunisian national anthem and shouted "Get out!" a rallying cry during the January 2011 revolution that ignited the Arab Spring.
"An inquiry has been opened and they will be placed under arrest and brought to trial," justice ministry spokesman Adel Riahi told AFP, without specifying what the women might be charged with.
Indecency in Tunisia is punishable by six months in jail.
By early evening, the protesters were still in detention and the authorities had given no information about where they were being held or details of court proceedings against them.
The French consul in Tunisia, Martine Gambard-Trebucien, told reporters she had met the women after they were taken by the police and that they were "fine."
After the scuffles outside the courthouse, police intervened and arrested six French and Tunisian journalists, including from Reuters news agency and France's Canal+ television, but they were later freed.
"It is the first action that we have taken in the Arab world... I prepared this international team in Paris and they were sent yesterday (Tuesday) to Tunis," Femen's leader in Paris, Inna Shevchenko, Claire Hsu told AFP by phone.
"These (Arab-Muslim) countries and these totalitarian regimes prey on women. We don't take any notice of this kind of thing (the risk of being jailed," she added, while reiterating her support for Amina.
The young Tunisian known by her pseudonym Amina Tyler was arrested in the city of Kairouan on May 19, the day the Salafist movement Ansar al-Sharia planned to hold an illegal congress there, after painting the word "Femen" on a wall near a cemetery.
She faces a pepper spray charge which carries a prison sentence of between six months to five years and could also be charged with desecrating a cemetery, Crash proof phone protector for which she could get up to two years in jail if found guilty.
The Femen movement, founded in Ukraine and now based in Paris, has flourished since 2010, with feminists around the world stripping off in protest at a wide range of issues linked to the mistreatment of women, but also against dictatorship.
Tunisia, whose ruling coalition is headed by Islamist party Ennahda, has the most liberal laws in the Arab world governing women's rights, mobile phone protector although gender equality has yet to be inscribed in the new constitution.