Environmentalists Friends of the Earth joined the libertarian group Taxpayers' Alliance in a late bid to derail HS2.
The two groups are normally at odds on policy, but both agree that the rail project is a bad use of public money, and likely to over-run its budget.
The projected price for HS2 is £56bn, but the Taxpayers' Alliance speculates that the final cost could reach £90bn.
The government says the line is needed to increase network capacity - and insists it will be built on budget.
The first phase of the railway is due to open in December 2026, with trains to travel at high speed between London and Birmingham before continuing on the existing West Coast Main Line.
The Department for Transport says the project will cut Birmingham-London journey times from 1hr 21min to 49min.
MPs are expected to give the scheme the final seal of approval this week when it returns to the Commons from the Lords.
But the libertarian lobby group says government-managed large infrastructure projects have a poor record of being delivered on budget, with one project in the USA overrunning by 190%.
In the UK, the Jubilee line extension was forecast to cost £2.1 billion, but the bill rose to £3.5bn, partly because of huge cost overruns during construction. Channel Tunnel costs swelled by 80%.
John O'Connell, chief executive of the Taxpayers' Alliance, said: "All the evidence shows that big government projects are delivered way over budget and almost never to deadline, so to allocate tens of billions of taxpayers' money to this white elephant is a big mistake."
In a 2014 paper, Bent Flyvbjerg, Professor of Major Programme Management at Oxford University, laid out what he called the iron law of megaprojects: "Over budget, over time, over and over again."
'Big infrastructure rarely delivers'
Friends of the Earth, who support high-speed rail when it diverts people from flying, say HS2 is the wrong scheme.
They complain it doesn't join up to HS1 - the line that joins London to the continent - so doesn't provide the possibility of getting on a train in the North and getting off in Brussels or Paris.Image copyright Reuters Image caption The plan has attracted criticism from local and national groups
Craig Bennett, FoE's director, told BBC News: "We think the money would be much better spent on a range of much smaller sustainable transport infrastructure projects to deliver real improvements to regular commuters and other train travellers over a far quicker timescale."
"Big infrastructure rarely delivers on its promises. That's why we think Hinkley C nuclear station is also a waste of money.
'Tough grip on costs'
"For the Hinkley subsidy, you could fund the mother of all national energy efficiency retrofit programmes for millions of homes. That would deliver carbon savings far quicker, would make a real improvement to peoples' lives."
The former Chancellor George Osborne kick-started the drive towards major projects as a way of creating jobs. HS2 is widely supported by councils in the North of England and has received backing by MPs across the parties.
The Department for Transport said: "HS2 will become the backbone of our national rail network - creating more seats for passengers, supporting growth and regeneration and helping us build an economy that works for all.
"We are keeping a tough grip on costs and the project is on time and on budget at £55.7bn."
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