Digging began after a fresh line of inquiry suggested 21-month-old Ben may have been crushed to death by a digger near a farmhouse his grandparents were renovating in July 1991.
Senior investigating officer Detective Inspector Jon Cousins, from South Yorkshire Police, said the 19-strong team expected to find “hundreds” of bones, all of which will be analysed in laboratories once they are recovered.
But he also refused to rule out that Ben may still be alive.
He said: “I am continuously keeping an open mind - and still do - as to what happened to Ben in 1991.
“There are still some other live lines of inquiry of what might have happened to Ben.
“All of this has resulted in a lot of myth and legend that has gathered over 25 years as to what has happened to Ben. It has allowed us to pare back and find out the truth and fact. That is why we’re here today.”
He added: “There are many lines of inquiry. I am keeping an open mind, but what I know at the moment with all the information we have, I’ve made the decision that it is necessary to do the work that we are going to be doing over the next week or so.”
Asked if he expected to find answers, Mr Cousins said: “I am optimistic about the search taking place.”
Investigators have already told Ben’s mother Kerry Needham to “prepare for the worst” ahead of excavation work beginning on the island.
Speaking from the site, senior investigating officer Mr Cousins said he had a “private” chat with Ms Needham, who is not in Kos.
He said: “I personally spoke to Kerry this morning and explained what I would be doing today. I had a private conversation with her around how she was feeling, and also explained the emotion that all of the team are feeling at this time. It is an event which quite clearly is not something to be excited about, given the circumstances, but we are optimistic about the work we are going to be doing.”
It came as Ben’s mother said the notion her son was dead never entered her “worst nightmares” until a mystery tip-off to police this year.
Ms Needham, from Sheffield, said: “Not even in my worst nightmares has Ben ever been dead ... until now. I’ve been waking up and finding my pillow wet with tears. This witness told police we deserve the truth - but we deserved the truth 25 years ago.”