The 21-month-old from Sheffield, South Yorkshire, went missing during a family holiday in July 1991.
A fresh excavation of farmland began on Monday, following new evidence that he may have been killed and buried there.
Police said they found "a vast number" of animal bones and small pieces of fabric which were "of slight interest".
A 19-strong team of South Yorkshire Police officers, forensic specialists and an archaeologist have been scouring the arid stretch of olive grove, which has been used for farming for generations.
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Ben was last seen playing on the land and it is close to where he vanished while his grandfather was renovating a property 25 years ago.
His family believe he was abducted, but police are now investigating whether he was accidentally run over and killed by a bulldozer.
Det Insp Jon Cousins, from South Yorkshire Police, said the team - joined by local search and rescue volunteers - had made good progress in recovering potential evidence.
He said: "We found, as expected, a vast number of bones yesterday. Each one was examined immediately, and each one was discounted there and then as being an animal bone.
"There are some other items that are of slight interest - the odd piece of fabric. That is being analysed and looked at, but there is slight interest.
"Everything is being carefully looked at."
He added: "We want to make sure: do they or do they not relate to any of the items Ben was wearing on that day?"
On the day Ben went missing he was wearing a white and green shirt and a pair of leather sandals.
The recovered items have been forensically collected and photographs sent to colleagues back in the UK before a decision is made on whether they require further examination and testing.
The search is expected to last about a week.

The number issued to people in Northern Ireland also doubled, in the largest monthly increase since the Brexit vote.
June's result has sparked a marked rise in the number of people applying for Irish and European Union passports.
November is normally one of the quietest months of the year for passport applications.
But the total number from Northern Ireland - 4,569 - was up by more than 600 from October.
Some 6,855 people people in Great Britain applied for an Irish passport in November 2016, a significant jump from 3,133 last year.
Applications from Northern Ireland went up from 2,267 in November last year to 4,569 last month.
Police searching for missing toddler Ben Needham on the Greek island of Kos have found pieces of fabric on land close to where he was last seen.
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More than twice the number of Irish passports were issued to people in Great Britain last month than in November 2015.