The Church of England has joined opponents of the Government's HS2 proposals.
It has warned that current plans for constructing the line between London, Birmingham, Manchester and Leeds means human remains will not be treated "in a decent and reverent manner".
The Archbishops' Council, which is led by the Archbishop of Canterbury and the Archbishop of York, said there must be changes to give greater protection to remains which have to be exhumed along the route.
In a "humble petition" to the House of Commons, the council said work authorised by the bill to bring in the project would involve the destruction of three burial grounds consecrated for the burial of the dead in accordance with the rites of the Church of England and the removal of human remains and monuments from them.
The petition said provisions in the bill did not do enough to ensure that, during and after the removal of remains, they were treated in a decent and reverent manner or that they were subsequently reinterred in consecrated land.
It added the bill did not make adequate provision to ensure any monuments which were removed were disposed of in a suitable manner.
"This is inconsistent with the approach taken in other legislation which provides for the compulsory acquisition of land and its use for statutory purposes," the petition said.
"Your petitioners therefore humbly pray your Honourable House that the Bill may not be allowed to pass into law as it now stands."
Other high-profile petitioners have also lobbied Parliament to stop the high speed rail scheme in its current form including Earl Spencer, brother of the late Diana, Princess of Wales, and Lord Rothschild, who both own land along the route.
They have complained that the link will cut through their estates, cause noise and damage areas of outstanding natural beauty.