Local authorities said in June that they were investigating a German man, named as Christian B, on suspicion of murdering Madeleine, who disappeared aged three from an apartment in 2007 while her family was on holiday in a resort in Portugal’s Algarve region.
Prosecutor for the northern city of Braunschweig, Hans Christian Wolters, said the new possible victim came forward following an international call for witnesses, German news agency dpa reported.
Christian B is now being investigated on suspicion of raping the Irish woman in the Algarve in 2004, he said.
The suspect, in prison in Germany in a separate case, spent many years in Portugal, including in Praia da Luz around the time of Madeleine’s disappearance.
He has already been convicted twice for previous “sexual contact with girls”, authorities say.
But they do not have enough evidence to hold him in prison on the evidence of Madeleine's case alone.
Mr Wolters said there is “no new situation” regarding the evidence on the McCann case, and would not give further details or elaborate on the nature of the evidence.
Madeleine is believed to be dead by German authorities. Mr Wolters told Portugal's RTP TV that evidence of Maddie's death exists.
TV presenter for Portugal's RTP station Sandra Felgueira asked him: "Do you have any material evidence that Madeleine is dead?"
Mr Wolters replied: "Yes." Ms Felgueiras then asked: "What evidence do you have for her death? Do you have a tape?"
But Mr Wolters refused to give any more details, saying: "I can't say anything about what we have."