The Crossrail Bill has finally finished its marathon passage through the House of Commons after almost three years.

The legislation is for what will be the largest civil engineering project since the Channel Tunnel underwent exhaustive line-by-line scrutiny after it was introduced in February 2005.

Rail Minister Tom Harris told MPs: “Crossrail has the potential to improve the lives of commuters as nothing has before. It will provide London and the South East with a world-class railway, delivering high-capacity main line rail services to and through the heart of the City and West End.

“It will provide a new fleet of trains, operating a 24 trains-an-hour peak service in both directions through central London, carrying some 200 million passengers a year.”

He said Crossrail would generate cash benefits to the UK economy of more than £20 billion – and possibly substantially more.

The project would generate thousands of jobs, drastically relieve congestion on the London Tube and Overground networks and support the capital’s development as the financial centre of Europe.

He said it was not possible to build such a large transport infrastructure project in a densely populated area without some adverse impacts on those living and working nearby. But he said they would be mitigated as much as possible, and were outweighed by the advantages Crossrail would bring.

Conservative spokesman Stephen Hammond described Crossrail as “a scheme of international importance to London”. And Liberal Democrat transport spokeswoman Susan Kramer said it would be “absolutely crucial to making sure that London continues its economic vibrancy.”

She added: “We would have loved it to go to Reading in the west and to Stansted in the east, but the project has at least made its beginnings.”

One dissenting voice came from Northampton Conservative MP Brian Binley who questioned the estimated £16 billion cost.

“I will bet any Member in the Chamber that that figure will end up at between £30 billion and £35 billion,” he said.

“I want it on the record that I believe that this will turn out to be an immensely costly exercise, both for London and the country, and the economic return will be nowhere near the return projected by the Government.”

Ms Kramer has previously warned that if there are any savings from Crossrail they must be returned to fare payers. She said that, as a chunk of the project was being paid for by passengers and London businesses, it was crucial they should get the benefit from any cost under-runs.

Transport secretary Ruth Kelly says she is confident the budget of £15.9 billion will be sufficient.