Dieter Krombach, 74, was convicted in absentia in 1995 of manslaughter in France over the death of 14-year-old Kalinka Bamberski, who died mysteriously at his home in Lindau in Germany while visiting with her mother in 1982.
The doctor was found on Sunday trussed up and bleeding from a head wound, in a doorway near the court in the eastern city of Mulhouse, just over the German border, police said.
The doctor's French legal counsel said his client had been taken against his will. "It was a kidnapping, my client was taken by force in Germany," said lawyer Francois Serres.
Kalinka's father, Andre Bamberski - who is convinced Krombach drugged his daughter in order to rape her and has lobbied for two decades for him to be jailed - was also arrested in Mulhouse.
Bamberski made an anonymous phone call to police about Krombach's whereabouts, he admitted to police during questioning. The German cardiologist was taken to hospital under police custody.
Bamberski set up a 300-strong pressure group, "Justice for Kalinka," that has campaigned for Krombach to be jailed for his daughter's killing.
The head of Bamberski's association, Robert Pince, said he believed the girl's father had tried to deliver Krombach to the courts.
"Of course I suspect Andre Bamberski of trying to bring Dieter Krombach back to France, even if I cannot say so for certain," he said.
"Andre Bamberski is a very religious man. He does not want revenge, he wants justice," Pince said. "He has been fighting for 25 years and maybe he felt the case was dying off. He may have wanted to give a good kick and stir things up."
Kalinka Bamberski was found dead at the doctor's home on the banks of Lake Constance one morning in July 1982, bearing needle marks on her arms.
German investigators questioned Krombach over her death, but they failed to establish the cause of death and the case was dismissed for lack of evidence the following month. But France reopened the case three years later after an autopsy on
Kalinka's exhumed body, carried out at her father's request, suggested foul play.
In 1995, Krombach was sentenced to 15 years for manslaughter and an international warrant was issued for his arrest.
But Krombach also won a 2001 case against France before the European Court of Human Rights, which ruled that he had been denied a fair hearing and the right to an appeal.
The doctor was handed a two-year suspended sentence by a German court in 1997 for sexually abusing a 16-year-old patient after injecting her with anaesthetic in his surgery. In 2007 he was convicted of fraud for continuing to practice medicine illegally after being stripped of his licence.