Archaeologists have accused Highways England of accidentally drilling a large hole through a 6,000-year-old structure near Stonehenge during preparatory work for a tunnel.

The drilling, which is alleged to have taken place at Blick Mead, around a mile and a half from the world-famous neolithic ring of stones, has enraged archaeologists, who say engineers have dug a three-metre-deep hole (10ft) through a man-made platform of flint and animal bone.

Highways England have said they are not aware of any damage to archaeological layers on the site caused by their work and will meet with the archaeological team on Thursday, led by David Jacques, a senior research fellow at the University of Buckingham.

Before the drilling incidents, archaeologists were concerned that the construction of a tunnel and a flyover near the site will cause the water table to drop, damaging remains preserved in water-logged ground. The Highways Agency agreed to monitor water levels as part of the project.

The 6,000-year-old platform through which a hole has been drilled preserved the hoof prints of an aurochs, giant prehistoric cattle that are now extinct.

Jacques said: “This is a travesty. We took great care to excavate this platform and the aurochs’ hoofprints. We believe hunters considered this area to be a sacred place even before Stonehenge. These monster cows – double the size of normal cattle – provided food for 300 people, so were revered.

“It the tunnel goes ahead the water table will drop and all the organic remains will be destroyed. It may be that there are footprints here which would be the earliest tangible signs of life at Stonehenge. If the remains aren’t preserved we may never be able to understand why Stonehenge was built.”

Blick Mead is part of the Stonehenge and Avebury Unesco world heritage. A Highways England spokesperson said: “We are not aware of any damage being caused to archaeological layers. We notified Prof David Jacques of the locations of our water table monitoring, and have adhered to guidelines in carrying out the work. We have also kept Prof Jacques informed and we will be meeting him on site [on Thursday].

“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.

“The works have been undertaken in a highly professional manner, with an archaeologist on site and with due care being exercised at all times.”