A tunnel at Stonehenge would have an "irreversible impact" on the landmark, says a group which advises Unesco on World Heritage Sites.
The International Council on Monuments and Sites UK (ICOMOS) said other routes outside of the World Heritage site should be considered.
The council also queried why the option of using Ministry of Defence land at Boscombe Down had been excluded.
Highways England said it would not comment on individual replies.
A spokesman did say some 6,500 replies had been received from the consultation.
The council added although it did not object to the idea, the consultation needed to be more robust and take into account that its World Heritage Status also included Avebury stone circle and other monuments.
It also suggested that the tunnel needed to be longer so it did not impact on the site and take away from its unique value.
It described the consultation options set out as "near identical", with only an option to have a northern or southern bypass for Winterbourne Stoke.
The report also highlighted another route across Boscombe Down which lies outside the WHO site.
It said: "No reason is offered in the current consultation for the exclusion of the RAF Boscombe Down land from areas to be considered.
"It has no other known specific designations or constraints beyond its ownership."
The council said more consideration had been given to the Blackdown Hills AONB status which protected the A303 being dualled and upgraded.
However, the World Heritage Status for Stonehenge, an international designation, was not being given the same privilege.
The land is currently leased to QinetiQ on behalf of the MoD until 2025, the council said.
The council added the length of the tunnel "appears to be based on cost rather than cultural heritage considerations".