Rose Kabuye was detained on her arrival at Frankfurt
Rwanda has expelled Germany's envoy and recalled its own ambassador amid a row over a detained presidential aide.
Foreign Minister Rosemary Museminali said the German envoy would not be welcome until the arrest of protocol chief Rose Kabuye was resolved.
Ms Kabuye was detained in Frankfurt on Sunday in connection with a killing that triggered the 1994 genocide.
She is one of nine senior officials wanted over the shooting down of former President Juvenal Habyarimana's plane.
His murder is widely seen as the spark that led to the deaths of some 800,000 people in Rwanda.
Ms Museminali told Reuters news agency that the action did not mean a cut in diplomatic ties.
"It's not a permanent move ... we've called our ambassador in Berlin to come for consultations, and we've asked the German ambassador to leave until this matter is resolved," she told the agency.
Earlier in the day, President Paul Kagame denounced Ms Kabuye's arrest as a violation of Rwandan sovereignty.
President Paul Kagame said the arrest would affect international ties
The Rwandan leader is in Frankfurt for a series of meetings with business leaders. Ms Kabuye was detained under a French arrest warrant when she arrived ahead of him to prepare for his visit.
Mr Kagame, who visited his aide in Preungsheim women's prison, argued that she should not have been arrested because her trip was made in an official capacity.
He called her arrest "a violation of the sovereignty of Rwanda".
In a statement, the African Union expressed "dismay and concern" over Ms Kabuye's arrest, saying she should have been entitled to immunity as she was on official business.
German authorities said they had no choice but to arrest the aide under the warrant issued two years ago by a French judge.
A state prosecutor, Hildegard Becker-Toussaint, emphasised that the charges against Ms Kabuye were very serious.
"When there's an arrest warrant out in France, we have no reason to doubt it," she said.
"We had no reason to believe that she had diplomatic immunity because she explicitly travelled privately."
Ms Kabuye denies any role in Mr Habyarimana's death but is likely to be extradited to France soon, German officials and her lawyer say.
French legal authorities have been investigating Mr Habyarimana's death because his aircraft had a French crew.
The arrest warrants led to an immediate break in diplomatic relations between Paris and Kigali, and tensions that have continued ever since.
On Monday, thousands of people turned out in the Rwandan capital to protest against the arrest of Ms Kabuye, a former guerrilla fighter with the Rwandan Patriotic Front (RPF), now Rwanda's ruling party.
The plane carrying Mr Habyarimana, a Hutu, was shot down on 6 April 1994, at a time of uneasy peace between Mr Kagame's Tutsi rebels and the Kigali government.
The radical Hutu government accused the RPF of carrying out the assassination. Within hours, militias set up roadblocks and started to systematically murder any Tutsis or moderate Hutus they could find.
The RPF has always accused the Hutu extremists of shooting down the plane to provide a pretext for carrying out their genocidal plans.
Some 800,000 people were slaughtered in just 100 days before Mr Kagame's forces ousted the Hutu government.
Mr Kagame has long accused France of complicity in the genocide by arming Hutu militias.