German authorities said in June that they had identified the German man as a suspect in the case of Madeleine, who disappeared from an apartment in 2007 while her family was on holiday in the resort of Praia da Luz in Portugal’s Algarve region, and were investigating him on suspicion of murder.
Braunschweig prosecutor Hans Christian Wolters said the new possible victim came forward following an international call for witnesses, news agency dpa reported.
The German man is now being investigated on suspicion of raping the Irish woman in the Algarve in 2004, he said.
The suspect, who is 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 two previous convictions for “sexual contact with girls”, authorities say, but they do not have enough evidence to hold him in prison on the strength of the McCann 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.