Students are protesting at the election of Monika Auweter-Kurtz as president of the University of Hamburg after accusing her of being an armaments researcher.
The university's council elected the 55-year-old physicist to take over the presidency from Jurgen Luthje. Students have named her "missile Monika".
The protests came after Professor Auweter-Kurtz, who heads the Steinbeis Transfer Centre for Plasma and Space Travel Technology at the University of Stuttgart, agreed to test materials for armament company Bayern-Chemie Protac. The materials were for use in rocket combustion chambers that can also be employed in warfare missiles.
Bela Rogalla, student representative on the university's academic senate, said: "The appointment not only harms the image of the university as a scientific institution but also counteracts the efforts of scientists and academics to encourage politics of peace."
The International Association of Lawyers Against Nuclear Arms also objected to Professor Auweter-Kurtz's appointment.
But the physicist, who was awarded the Federal Cross of Merit - Germany's highest honour - rejected the accusations, saying she carried out basic research on combustion chambers as part of a larger project that was not necessarily meant for military purposes.
She added: "Working together with an armaments firm has nothing to do with leading a university. Former presidents were possibly once members of the Army. If I were a man, I would certainly have had to do military service."
Ursula Plazer, a member of the findings commission and director of the dental clinic at the University of Eppendorf, also defended the choice. She said: "Professor Auweter-Kurtz does not carry out direct research on rockets."