Victoria Police shifted focus to Buninyong Bushland Reserve, 11km from the regional city, on Wednesday.
Ms Murphy was last seen leaving her home to go for a run on the morning of February 4.
Police allege 22-year-old Patrick Orren Stephenson murdered her at Mount Clear on the day she went missing.
Mount Clear, a semi-rural suburb, is 6km from where police have focused their search.
Crime Command Detective Acting Superintendent Mark Hatt said multiple resources had been directed at 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."
Police relaunched the search on Wednesday based on new intelligence from multiple sources.
Ballarat mayor Des Hudson said he hoped a successful search could bring some closure to the Murphy family.
"Our thoughts are with the Murphy family because every time this issue is back in the media, they would no doubt ride the roller coaster of emotion, waiting and hoping that Sam can be found," he told AAP.
Stephenson, a tradesman, was arrested earlier this month on the outskirts of Ballarat.
He 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.
After Ms Murphy disappeared, a search began around Ballarat involving trained emergency services workers and hundreds of concerned locals.
They combed dense bush, private land and walking tracks and police set up a base at Buninyong Police Station.
