Detectives said they were approached by the owner of the farmland currently being scoured for clues on the Greek holiday island of Kos, about the discovery of suspected ancient tombs there.
Forensic specialists and an archaeologist have been combing an arid stretch of farmland where 21-month-old Ben was playing a quarter of a century ago.
The excavation began after new evidence was found that the Sheffield toddler may have been killed and buried there, yards from where he vanished while his grandfather was renovating a property.
But officers said their investigation was continuing despite the worries of the landowner, as they had not been contacted by a magistrate.
South Yorkshire Police’s Detective Inspector Jon Cousins: “I was approached yesterday on the 29th September by Mr Troumouchis, the owner of the land on which we are currently conducting the search to find answers for Ben’s family and the people of Kos.
“He raised with me concerns about the discovery of what appear to be ancient tombs. So far I have not had any contact from the magistrate to say that we must stop conducting the important work we are doing on site.
“My priority is to ensure that disruption to the operation that my team are running remains at an absolute minimum. If magistrates’ permission is withdrawn, it will be my intention to seek immediate judicial authority to search this area of land.”