But German prosecutor Hans Christian Wolters would not disclose what evidence he had that led police to that conclusion.
Wolters told British tabloid The Mirror that he had “re-established contact” with the McCann family in writing.
“We, of course, really consider the fact that it is going to be very hard for the family when we tell them we assume Madeline is dead,” he said.
“But we can’t say why she is dead.
“It is more important that we are successful and we are able to get the culprit, as opposed to just putting our cards on the table and tell them why we think she might be.”
Madeleine went missing in May 2007 while on holiday in Portugal with her family.
She was aged three at the time of her disappearance.
Last week, Wolters said his office had “findings” that showed a 43-year-old male suspect had murdered Madeleine.
“At the moment, there is insufficient evidence to convict,” he said.
Although he did not mention the suspect by name, European media has reported that man as German national Christian Brueckner.
The new alleged suspect is serving a seven-year prison sentence for the rape of a 72-year-old American woman in 2005.
His attorney, Friedrich Fülscher, told The Times that his client is “remaining silent on the allegation at this time on the advice of his defense counsel”, calling it “quite common in criminal proceedings”.
“It is the duty of the state to prove that a suspect committed a crime,” the lawyer added.
“No accused person has to prove his innocence to the investigating authorities.
“After we have examined the files, we will see how to proceed.”
Brueckner had reportedly lived in Portugal’s Algarve region from 1995 to 2007, and also resided in a house in Praia da Luz, the resort town where Madeleine disappeared.
The Times reports investigators are examining whether there is a link connecting Brueckner to an incident involving a 10-year-old British girl in the same resort in 2005.
London’s Metropolitan Police last week revealed details of two cars linked to the suspect around the time of Madeleine’s disappearance, and called on the public to step forward with any information about them.
With AAP