Ben was 21 months old when he went missing while on a family holiday on the Greek island of Kos in 1991.
His mother Kerry has always maintained her son is alive and was probably abducted and has vowed to find him.
South Yorkshire Police said it would use the funding to "commit further resources to the investigation".
In a statement, South Yorkshire Police and Crime Commissioner Dr Alan Billings said the funds would "continue to support the Greek authorities in the search" for the missing toddler.
"Ben's mum, Kerry, has spent more than 23 years searching for her son," he said.
He added: "I fully support South Yorkshire Police in their ongoing pursuit of the facts. They have worked hard in facilitating the Greek investigation into Ben's disappearance but there is still more work to do."
Det Supt Matt Fenwick said the force was working to "establish the right investigation team, with a view to the inquiry commencing in April".
He said: "[Ben's] family has endured untold pain and anguish in the years that followed and have never given up in trying to find him.
"South Yorkshire Police has provided support to the Greek authorities wherever requested in assisting with the investigation.
"We hope that by continuing to work with them, we can assist in providing the answers Ben's family so desperately want."
A Home Office spokesperson said it was "committed in its support for the search".
Ben vanished on 24 July 1991, after travelling to Kos with his mother and grandparents who were renovating a farmhouse in the village of Iraklise.
Two years ago a DNA test was carried out on a man in Cyprus in an attempt to establish if he could be the toddler, but proved negative.
In 2012, a police operation focused on a mound of earth and rubble close to where Ben was last seen, but no trace of him was found.
A police force has secured £700,000 from the Home Office to continue investigating the disappearance of Sheffield toddler Ben Needham.