The excavations near the World Heritage Site have prompted angry campaigners to suggest the planned 1.8-mile (2.9km) underground dual carriageway is a "done deal".
Highways England said it was "fact-finding work and not construction".
Plans for the road were unveiled by the government this month.
The busy A303 currently passes within a few hundred metres of the ancient monument and the tunnel would remove much of the road.
Dr Kate Fielden, from Stonehenge Alliance, said: "Highways England is pursuing this scheme before they've even finished the archaeological excavation - it's like it's a done deal.
"It would have been nice to have a full account of the work being undertaken, its results and investigations.
"Most worrying of all is the location, it is right below the ancient avenue which is a key feature of the pre-designed prehistoric landscape. It's a philistine way of treating the landscape."
Dr David Jacques, from The University of Buckingham, has been leading an archaeological project at nearby Blick Mead since 2005.
He said: "There's no sense of balance in this consultation. It seems to be simply Highways England explaining what they are going to do.
"They are putting a lot of energy into this but Blick Mead and the local landowners have yet to be invited into the consultation process."
A Highways England spokesman said: "We are undertaking geotechnical and archaeological surveys in and around the Stonehenge World Heritage Site.
"These will add to the evolving knowledge and understanding of this unique landscape and help us identify any issues when taking forward options for detailed assessment and design."
A public consultation to gather views of drivers and residents runs until 5 March.
Diggers have been spotted at the proposed site of a controversial tunnel near Stonehenge - before the end of a public consultation about the project.