Leader of Bradford Council, Susan Hinchcliffe has written to Mr Shapps as she said the Department for Transport (DfT) may have breached planning rules and has sent one of their engineers to the historic tunnel to make an emergency assessment of its condition.
The tunnel, which links Holmfield to Queensbury, was once part of the Great Northern Railway's route from Halifax to Keighley, and was completed in 1878.
But it was closed to all traffic in 1956 as part of a post-war cost-cutting drive, and the track was lifted in 1963. Now a planning application from Highways England would see it filled in and sealed.
But this has received more than 4,000 objections and Ms Hinchclifee said was “one of the most commented on applications Bradford Council has ever processed”.
Campaigners instead want to see it incorporated into the Bradford to Halifax greenway cycle route
In the letter, she asks for an immediate halt to the plans at the Victorian tunnel and for an independent third party evaluation to assess its condition and use of emergency powers.
She also requested that Highways England withdraw a planning application to seal other shafts at the tunnel, and that representatives of the Department of Transport visit Bradford and the site to discuss funding options.
Last week, Highways England’s contractor moved onto the historic site and began filling in one of its air shafts. And the council then sent an urgent hand-delivered letter to Highways England saying the correct planning process had not been followed.
Ms Hinchcliffe, said: “Campaigners for the tunnel have been brilliant and we are all backing them.
“The actions of Highways England, which have happened without warning, have put the whole project in jeopardy.
“We need them to halt all the works and withdraw the planning application to seal the tunnel.”
The letter added: “We have a once in a lifetime opportunity to save this unique asset of our Victorian industrial heritage and restore it as part of a nationally recognised cycleway that will become a national visitor attraction in its own right.”
Norah McWilliam, leader of the Queensbury Tunnel Society, said: “Highways England appear hell-bent on mindless destruction. They have abused emergency powers on the premise that a minor defect close to a shaft - which has not deteriorated meaningfully in three years - could implausibly trigger a catastrophic collapse. They must be held accountable for their actions.
“Intervention by the Secretary of State for Transport is long-overdue, with the genuine intention of getting maximum public benefit from the tunnel.”
The DfT was contacted for comment.