The organisation favours a tunnel, saying it offers the best economic benefits and journey time improvements.
But audience members at a BBC debate said its consultation made it hard to respond favouring the alternative plan.
Highways England said people could comment if they favoured other routes.
Highways England favours "Option C" - a tunnel between Gravesend and Tilbury - while the only remaining alternative is "Option A", a new crossing at Dartford.
The proposed road tunnel would run from the M2 to the M25 in Essex, running under the Thames east of Gravesend into Kent.
The consultation states that a Lower Thames Crossing is needed to reduce congestion at the existing Dartford Crossing and asks for views on Highways England's proposed route.
Critics said it was "a sales brochure for Option C" put out by Highways England.
"The way you have presented all this information makes it so hard for people to say that they want Option A that it is an invalid consultation," the Reverend Nigel Bourne, vicar of St Mary's Church in Chalk, told Highways England at the debate in Shorne Village Hall.
The church website directs users to a petition protesting at the proposal.
Option B, which would have connected the A2 at Swanscombe in Kent with the A1089 in Essex, was dropped in 2013.
The public consultation, which started on 26 January, runs until 24 March.
Consultation manager Martin Potts said the questionnaire asked open questions about other routes people might favour.
But he said: "It would be completely inappropriate for Highways England to present material that indicated all the routes and all the options we have assessed are equally viable."
The full Lower Thames Crossing Debate will be broadcast on BBC Radio Kent at 19:00 GMT on Friday and 11:00 GMT on Sunday.
Opponents of plans to build a Lower Thames Crossing east of Gravesend have called the public consultation invalid - branding it a sales brochure for Highways England's preferred option.