Highways England intends to build a new dual carriageway through the Rimrose Valley Park to serve a planned new deep water container port at Liverpool.
The body put forward two options for public consultation, upgrading the existing road or building a new dual carriageway.
But Sefton Borough Council said building a five kilometre long tunnel under the park was a better option and should have been included in the consultation.
The council was given permission to seek a judicial review in February.
Sefton argued that the tunnel option was "realistic and not unaffordable" and local people should at least have been allowed to express their support for it.
Council leader, Ian Maher, also argued that the government was willing to "lavish taxpayers' money" on London’s Crossrail project.
"Our communities deserve the same consideration and need to benefit from the port expansion and not suffer as a consequence," he argued.
Highways England said it had a total budget of "around £250 million" to upgrade road access to the port - and that building a tunnel would cost between £620 million and £1.2 billion.
That cost "would outweigh the economic benefits and represent poor value for money", it insisted.
Dismissing Sefton's challenge last week, Mr Justice Kerr said: "Highways England informed interested parties what it was considering and why.
"It gave a clear and simple explanation of why it did not consider the tunnel option to be viable: it was too expensive and regarded as poor value for money."
The tunnel option was viewed as impractical, and the judge ruled: "I do not find any unfairness in the government and Highways England taking that position."
He added: "The argument that the tunnel should not be regarded as unaffordable is a political rather than an economic one.
"The council reproached the secretary of state for lavishing taxpayers' money on Crossrail, while depriving the Sefton area of much lesser sums that would avoid severe environmental damage and give proper weight to the well being of local residents.
"That is a political argument. The council did not make an economic case to meet the government's argument that a tunnel would be too expensive.
"It did not challenge the proposition that the cost lay far beyond the allocated budget for the project."
The judge told the court: "The funding of infrastructure projects such as this one is a matter for government, not the court.
"The balance to be struck between environmental protection and economic regeneration is par excellence a matter for the executive."
Mr Justice Kerr concluded that the final decision whether or not to grant a development consent order (DCO) for the new road had yet to be made by the secretary of state. The DCO application was submitted in October last year.
And he rejected arguments that the court's decision - and the government's 100 per cent ownership of Highways England - made the outcome a "foregone conclusion."
"The economic, political and environmental arguments, not to mention the budget, may have changed by the time any DCO application is determined", he said.