Highways England engineers monitoring water levels dug the 3.5 metre deep bore hole through the prehistoric platform.
Blick Mead, which is about a mile from Stonehenge, was unique in Western Europe and could have been crucial to understanding why Stonehenge was built where it was, he added.
"We are not aware of any damage being caused to archaeological layers", said a spokesperson for Highways England in a statement. David Jacques, the lead archaeologist, told the BBC that engineers did not consult him before starting the work.
Highways England is now constructing a highly-controversial £1.6bn ($2bn) upgrade of the A303 road, which links the M3 from London to the M5 in the south west.
The tunnel, part of an effort to solve a decades-old traffic problem at Stonehenge, has been widely criticized by archaeologists and the local community.
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Perfectly preserved hoof prints of wild cattle known as aurochs have recently been found at the Blick Mead encampment in Wiltshire.
Construction on the tunnel and linking flyover would lower the water table, drying out the peat and silt conditions which preserve archaeological remains, he added.
A senior research fellow at the University of Buckingham called the situation a "travesty". He anxious that if the construction goes ahead, organic remains and evidence of monster cows that lived in the area would be destroyed. "If the remains aren't preserved we may never be able to understand why Stonehenge was built". "We took great care to excavate this platform and the aurochs' hoofprints", David Jacques, professor of archaeology at the University of Buckingham, who discovered the site 12 years ago, said of the reported damage.
Jacques and representatives of Highways England are meeting at the site on Thursday to assess any damage.
"Our assessments so far indicate that construction of the scheme will have no significant effects on the Blick Mead area, and we are undertaking this further hydrogeological investigation at Prof Jacques' request".
Campaigners fear work could destroy archaeological treasures in the area.