South Yorkshire Police said that officers formally ended their search on the island of Kos yesterday afternoon.
Ben, from Sheffield, disappeared on 24 July, 1991 after travelling to the island with his mother and grandparents.
The latest search operation was prompted by information that digger driver Konstantinos Barkas, also known as Dino, may be responsible for the toddler’s death.
He was clearing land with an excavator near where Ben was playing on the day he vanished.
Mr Barkas is believed to have died from stomach cancer last year. Over the past three weeks, digs took place near the farmhouse where he was last seen and a second site 750 metres away.
More than 800 tonnes of soil was dug up, with items of interest sent back to the UK for forensic analysis.
Detective Inspector John Cousins, who is leading the investigation, said: “I’ve got the confidence that we have done exactly what we can, given the plans we had before we came out here so that I can give an answer, whatever that might be, to Ben’s family.”
He said he was proud of his team: “It has been a difficult job, the conditions have been extremely hot and very dusty and they are long hours they have been working.”
In a statement, South Yorkshire Police said: “The physical search of two sites on Kos, Greece has formally come to an end.
“Work continues behind the scenes as officers begin to process the findings from each site.”
The force said a full update will be released from the team on the island at midday UK time today.
The Help Find Ben Needham campaign thanked South Yorkshire Police, Hellenic search and rescue workers and the media for their work over the past three weeks.
A variety of theories on Ben’s fate and reported sightings have arisen since his disappearance and his mother, Kerry Needham, had been holding out hope that she would one day be reunited with her son.
Earlier this year, South Yorkshire Police received extra funding from the Home Office to help in the search for Ben.
Ms Needham has been forthright in her support of the investigation.
Just last week, she said she believed her son would not be found alive.
She told ITV’s Good Morning Britain that she and her family are “tired and distressed” and cannot live for another 25 years without knowing what happened to Ben.
Two weeks into the search, detectives said they had accumulated more than 60 items of interest that they would bring back to the UK for forensic testing.