From there she was transferred to the main law courts in Paris to appear before Marc Trevidic, an anti-terrorism investigating magistrate, Bernard Maingain, Kabuye's lawyer, told the AFP news agency.
Judicial officials confirmed that Kabuye was put under judicial investigation - in effect, charged - with "complicity in murder in relation to terrorism".
She was later released on condition she not leave France without permission and appear when requested by magistrates, her lawyers said.
|Kagame, left, has condemned the arrest
of his chief of protocol [AFP]
"I'm not so scared because I am very innocent," Kabuye said on the France24
television news channel after being released.
"I know that when I get a chance to explain what happened everything will be okay, so I am not scared."
Habyarimana's death sparked a genocide which consequently engulfed the country.
Authorities in France began investigating the attack because the two pilots of the aircraft were French.
They suspect Kabuye of housing the Tutsi commando unit blamed for shooting down the jet.
Hutus killed more than 500,000 people, mostly minority Tutsis, before fighters led by Kagame drove them from the country.
His government claims that France armed the Hutu militias and former government troops who led the genocide.
Thousands of Rwandans turned out to protest in Kigali, the country's capital, on Wednesday against the expected extradition.
Yvonne Ndege, Al Jazeera's correspondent in Kigali, said: "There has been a huge amount of public anger over the extradition ... she is considered a heroic figure here.
"People have been protesting all over the country. They are demanding an immediate release of Rose Kabuye and a repatriation of her to her home in Rwanda.
"All evidence that we have seen is that most of these protests have been organised by community leaders and individuals who are simply outraged by her arrest.
"Bear in mind that she is credited with being part of the new government that put an end to the genocide here in 1994. Women have been chaining themselves to the gates of the German embassy here."