However, Mr McLoughlin argued the line was not "some expensive add-on" but a scheme which would help people with their daily lives.
Speaking at the National Rail Conference in Manchester, the MP said:
"As the impact of this week’s storm in the south shows, when trains are crowded and disrupted, life for hardworking people gets more difficult. That’s why the new north-south line isn’t some expensive add on. It’s about helping people with their daily lives.
"It’s needed to help commuters who now have to stand - and will soon have to queue - to get on their trains. It’s needed to help the cities of the north which want to compete on equal terms with London. It will be the new backbone of Britain."
Transport Secretary Patrick McLoughlin said the current weekend disruption on rail networks shows why upgrading the current rail system is not a viable alternative to the HS2.
He told ITV Daybreak the delays and disruption that occurred during the £9 billion upgrade to the West Coast Main Line proves why a new system is preferable to trying to increase capacity on the current network.
Transport Secretary Patrick McLoughlin is accusing Labour of "playing politics with our prosperity" over the £50 billion HS2 high-speed rail project.
Mr McLoughlin said those in opposition "learn nothing from the past," adding that the Labour Party could not claim to want one nation "if you won't back the things that will bring it together".
Labour appears to be cooling towards the HS2 project, which will see the scheme's first phase run from London to Birmingham in 2026, with a second Y-shaped route due to be completed to northern England in 2032/33.
Transport Secretary Patrick McLoughlin said he has "no doubt" the controversial High Speed 2 rail scheme will benefit the whole country, after claims it could cost some cities hundreds of millions of pounds.
Mr McLouglin said the project was "vital" for the economy's long-term health, adding: "It's of no doubt to me that it's beneficial to the UK. We need to make sure our cities in the north are able to compete with the rest of Europe as well."
HS2 will provide a £15 billion boost to the UK economy every year after it is built, the Government claims.
Transport Secretary Patrick McLoughlin will argue the network will relived the pressure on Britain's transport system and insist the project will be completed within its £42.6 billion budget.
"The main reason we need HS2 is as a heart bypass for the clogged arteries of our transport system," McLoughlin will say.
Ministers are attempting to bolster support for the train link, which will connect London with Birmingham, Leeds and Manchester, after it came in for withering attacks from the influential Public Accounts Committee.
Transport Secretary Patrick McLoughlin has defended the expected rise in rail fares next year saying that the rail network is in need of "huge investment". He told the BBC:
Nobody likes to see rail fares go up. I don't like to see it and passengers don't like to see it. We are massively investing in the railways, with £130 million being spent here at Nottingham, £800 million at Reading and £600 million at Birmingham.
– Patrick McLoughlin, Transport Secretary
Pressed to say when the government plans to end above-inflation fare rises, he said that the Office for Budget Responsibility has a target to do so in 2015.
He said that just over £8 billion was raised by ticket sales and just under £4 billion by taxpayers for the UK's rail services.
A Government minister and his department boss will face a grilling from MPs today over the West Coast rail franchise fiasco.
Members of the House of Commons Transport Committee will be armed with a damning initial report into what Labour has described as a "shambles" of a bidding process.
Transport Secretary Patrick McLoughlin and Department for Transport (DfT) permanent secretary Philip Rutnam will have to explain why the DfT went ahead with the West Coast bidding competition knowing the process was flawed.
Mr McLoughlin will also be asked why he told MPs on his first appearance before the committee in September that he was happy with the bidding process only for him to scrap the entire West Coast refranchising process a few weeks later.