A multi-billion pound cross-London rail link is vital, not just for the city, but for England, the government says.
London will struggle with increasing passenger numbers, Mr Darling said
MPs were debating the Crossrail Bill, which would give powers to build and run the project from Berkshire to Essex through underground tunnels in London.
The transport secretary said it would provide both a vital link in the national rail network, and extra room on London's overcrowded trains.
First proposed in 1989, Crossrail has been repeatedly delayed or shelved.
The intention is to link existing surface routes in Maidenhead, Berkshire, and Heathrow Airport in the west out to existing tracks in Shenfield, Essex, and Abbey Wood in south-east London, although the route is not fixed.
They would run through tunnels beneath London, connecting to new stations at Paddington, Bond Street, Tottenham Court Road, Farringdon, Liverpool Street, Whitechapel and Canary Wharf.
Rush hour demand
Transport Secretary Alistair Darling said it would be controversial, but London was relying on railways built by the Victorians and needed to meet the needs of the 21st Century.
He said: "The Bill will provide powers needed to build Crossrail, a new railway that will bring benefit not just to London but the south east and the wider part of the United Kingdom."
He added that the current system struggled to meet rush hour demand and something needed to be done about overcrowding.
"If we don't do anything there is a very serious prospect that at some point in the next decade, and certainly the one after it, London will simply not be able to carry the number of people that come into it," Mr Darling said.
But it would take "some considerable time" to get the Bill through, Mr Darling told MPs.
The Bill was introduced in the last Parliament, but had to be carried over due to a lack of time. Crossrail is not due to open until 2013 - a year after London hosts the Olympic Games.
Shadow Transport Secretary Alan Duncan asked what guarantees there were that the money would be available to finish the scheme as a report had shown a £7bn funding shortfall.
Some MPs saw the project, now estimated as costing between £15bn and £16bn, as an "historic opportunity".
But Bethnal Green and Bow MP George Galloway said it would have a devastating effect on his east London constituents.
He said: "The residents and small businesses of my constituency will be paying the greatest price for a service designed to connect Canary Wharf to Heathrow Airport.
"It will be like a major bombing raid on the East End: Three major tunnelling sites, a two-metre wide conveyor belt, 24 hours a day, seven days a week, for six years, carrying spoil from the digging of these three tunnel sites, going inches from people's windows."
And Lib Dem MP Tom Brake said the Bill could transform the public transport system - but would need detailed scrutiny.
"London has already had inflicted on it one Millennium Dome and it cannot afford another," he said.
The Bill gained its second reading, a debate on its general principles, on Tuesday night by 394 to 24.