Police moved their efforts to Buninyong, 11km from the regional city on Wednesday morning.
Ms Murphy was last seen leaving her home to go for a run on the morning of February 4.
Victoria Police allege she was murdered by 22-year-old Patrick Orren Stephenson, at Mount Clear, on the day she went missing.
Mount Clear, a semi-rural suburb, is six kilometres from where police have focused their search.
Detective Acting Superintendent Mark Hatt, Crime Command said all available resources were being poured into the search.
"Since Samantha's disappearance, extensive searches have been conducted in the Ballarat area and today we will focus on an area of bushland in Buninyong," he said.
"We will have a range of specialist resources involved, however as we are searching for Samantha's body, we ask that members of the public do not try and join today's search."
Stephenson, a tradie was arrested earlier this month on the outskirts of Ballarat.
Stephenson is the son of former AFL player Orren Stephenson, who played 15 games for Geelong and Richmond between 2012 and 2014.
The family home is in Mount Clear, where he often stayed, while he lives in Scotsburn, about 16km from Ballarat.
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