The 6,000-year-old Blick Mead site, situated around 1.5 miles from Stonehenge, has reportedly suffered damage from a 3.5 metre hole drilled through a platform.
Lead archaeologist at the site, Professor David Jacques, described the damage as a ‘travesty’, and said future work would ruin prehistoric animal footprints found at Blick Mead.
He told the BBC: ‘We took great care to excavate this platform and the auroch’s hoofprints.
‘If the tunnel goes ahead the water table will drop and all the organic remains will be destroyed.
‘If the remains aren’t preserved we may never be able to understand why Stonehenge was built.’
Highways England, who are undertaking preparatory work at the site, insist there had been no archaeological damage and engineers had ‘adhered to guidelines’.
A spokesman said its water table monitoring scheme ‘will have no significant effects on the Blick Mead area’.
Prof Jacques, who said engineers did not consult with him before carrying out work, is set to meet with inspectors to assess the site.
The Government wants to build a 1.9-mile (3km) tunnel past Stonehenge to hide the busy A303 as part of a £1.6bn upgrade programme.
Campaigners fear work could destroy archaeological treasures in the area.