The Democratic Green Party said Andre Kagwa Rwisereka had been found near his abandoned car and that his head had been almost completely severed from his body.
The party has been unable to register for presidential elections next month.
Human rights groups have accused the government of clamping down on the opposition before the vote.
Green Party Chairman Frank Habineza told the BBC: “We are calling upon the Rwandan government to use all means possible to find out the cause of his death.”
Mr Habineza said his body was found 3km from the town of Butare, where his car was located.
A police spokesperson has confirmed the death but suggested that robbery might have been the motive.
“People who saw him that night say he had a lot of money,” said police spokesman Eric Kayiranga, Reuters news agency reports.
Last month, former Rwandan army chief Lt Gen Faustin Kayumba Nyamwasa, who had fallen out with President Paul Kagame, was shot in South Africa.
His family have said it was an assassination attempt – allegations which have been denied by the Rwandan government.