The Transpennine Route Upgrade includes a remodelling of Huddersfield Station and knocking down, replacing or improving eight bridges between Huddersfield and Westtown in Dewsbury as well as widening and electrifying the line.
Network Rail says it will mean more seats, more trains and faster journeys between Manchester and York via Huddersfield and Leeds.
But the improvements will also cause significant disruption lasting several years, potentially affect flagship housing schemes and lead to the felling of hundreds of trees along the route.
Addressing a meeting of full council in Huddersfield Town Hall senior officers said: “It’s crunch time now.
“We need to get to a point where we understand exactly what is being proposed and what impact that’s going to have on our residents - not just during construction but when it’s built, as well.”
They said the authority was supportive of the investment coming into the borough but it wanted to ensure that everybody - residents, businesses and commuters - benefited.
They described the project as “big money coming into the Kirklees area” and “the Holy Grail in terms of rail connectivity”.
But they warned that even though consultation had taken place between the council and Network Rail, staff had “significant concerns” that had “not been resolved to our satisfaction”.
Those concerns included the huge loss of trees along the route, which had not been “adequately quantified”, and the impact of what was described as “significant earthworks” alongside waste sites on Emerald Street in Huddersfield and Weaving Lane between Ravensthorpe and Dewsbury.
Officers said: “There’s going to be a large programme of construction over several years. We need to know what that is going to be, when it’s going to happen and what we can do to mitigate that so that, as far as possible, residents can go about their business.”
They said making a formal objection - which will go to Transport Secretary Grant Shapps - would strengthen the council’s position.
That could mean a public inquiry in November “to best represent and uphold the council’s interests”.
They added: “It brings Network Rail to the table and the onus is on them, as well, to try and negotiate.”
Officers said the council had two options: to go with the proposals and work with Network Rail, or to object as a council to Network Rail’s Transport and Works Act Order Application, which was submitted to the government in March.
The move received cross-party support and was approved via a unanimous vote.
The TRU involves removing several bridges between Huddersfield and Westtown in Dewsbury - as well as the felling of 900 trees near Deighton Station.
Stations in Mirfield, Ravensthorpe and Huddersfield will be also remodelled.
To deliver its plans Network Rail decided to turn its car parks near Huddersfield Station into “strategic compounds” to support construction work.
That effectively scuppered the council’s plan to link the station to the vast St George’s Warehouse, and to provide park and ride facilities with pedestrian links to the station and town centre.
There have also been warnings that the upgrade will damage one of the council’s flagship housing schemes, the 4,000-home development at Dewsbury Riverside.