Head prosecutor in Braunschweig, Hans Christian Wolters, said the co-operation between the Portuguese and German authorities during the operation was "very constructive".
His words came after The Sun newspaper reported that samples had been taken from last week's searches after claims that bones and clothing fibres were found.
The newspaper reported that the bones were initially deemed to be animal remains but have been retained by prosecutors to be forensically examined.
The latest hunt for evidence came 18 years after three-year-old Madeleine disappeared from the Portuguese resort of Praia da Luz while on holiday with her family in 2007.
She was left sleeping by her parents, Kate and Gerry McCann, and vanished as they went for dinner in a nearby restaurant.
Search teams concluded their operation in neighbouring Atalaia, near the city of Lagos, after three days of scouring scrubland and abandoned structures.
German prosecutors requested the search as part of their continued attempts to source evidence to implicate prime suspect Christian Brueckner.
He is in prison for raping a 72-year-old woman in Praia da Luz in 2005 and is due to be released from jail in September if no further charges are brought.
According to reports, Brueckner sent a letter to police saying "decisive questions can never be answered".
Another letter shows the suspect telling Mr Wolters that "the investigation will be dropped", The Sun reported.
In October 2024, he was cleared by a German court of unrelated sexual offences, alleged to have taken place in Portugal between 2000 and 2017.
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