Completing the electrification of the Great Western line between London and the West is a top priority, the Transport Secretary has announced.
It means that two other major schemes - in the Midlands and across the Pennines - will be delayed.
Patrick McLoughlin told MPs that delays and problems, which have seen the costs treble to £1.7bn, "could and should" have been foreseen by Network Rail, whose chairman is being replaced.
Later, he told Bristol East MP Kerry McCarthy there were "big engineering challenges" but new trains should be operating on the electrified line in 2017 or 2018 (a year later than originally planned).
A train traveling from London Paddington became stuck in floodwater at Pound Pill in Corsham in the early hours of this morning. 90 passengers were on the train, which came to a halt in a cutting where water was up to a metre deep in places.
All the passengers were rescued from the train by 0600 this morning.
The train is still blocking the track causing major disruption to rail services in the region.
Services to and from Bristol Temple Meads are unable to call at Chippenham. Trains are being diverted via an alternative route, adding around 45 minutes to journey times.
There is disruption on CrossCountry trains between Cheltenham Spa and Bristol Parkway because of a derailed train.
Their services are being diverted via Gloucester station causing longer journey times, and there's no estimate for when the line may reopen.
This will also affect First Great Western services.
Passenger groups and unions have reacted angrily to news that rail fares are to rise by more than inflation from January.
The RMT and Action for Rail organised demonstrations at Bristol's Temple Meads station on Tuesday morning over the 4% increase.
Opponents claim fares have risen three times faster than wages in the last six years.
The Government says it's investing heavily in the railways.
Mike Hewitson from Passenger Focus spoke to ITV News West Country:
Rail fares are increasing nearly twice as fast as incomes, outstripping wages by almost 14 percent since 2007, according to the Campaign for Better Transport.
This graph shows how rail fares and incomes became decoupled in 2007, with rail fares soaring far above increases in earnings.
The group also says that next year will be the eleventh successive year in which rail fares have risen above the level of inflation.
The slight drop in the rate of inflation is due to air fares and price movements in the recreation, culture, clothing and footwear sectors, according to the Office for National Statistics (ONS).
A rise in petrol and diesel prices partially offset the fall, the ONS said.
Regulated rail fares in England are set to rise by an average 4.1% from January after the headline rate of retail price index inflation fell to 3.1% in July from 3.3% in June.
The rate of consumer price index inflation fell to 2.8 percent in the year to July 2013, down from 2.9% in June, according to the latest figures from the Office for National Statistics.
The number of rail passenger journeys has increased dramatically from around 750 million per year to 1.5 billion, according to Transport Secretary Patrick McLoughlin.
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:
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.