Network Rail's chief executive told the BBC that the plan, which was launched in April last year as the "largest modernisation of the railways since Victorian times", was too ambitious.
Mr McLoughlin also said Network Rail's chairman would leave the group.
Richard Parry-Jones will leave after his three-year term at Network Rail, which controls 2,500 stations as well as tracks, tunnels and level crossings.
He will be replaced by Sir Peter Hendy, the current commissioner of Transport for London.
'Significant challenges'
The projects at most risk of being delayed are the electrification of the Great Western Railway to Swansea, as well as the electrification of the Midland Mainline.The chief executive of Network Rail, Mark Carne, told the BBC the challenges of delivering myriad improvement projects - such as the electrification of the Great Western line to South Wales, improved punctuality for millions of passengers and the renewal of hundreds of miles of track - while still running a railway seven days a week were simply overwhelming.
"Over the last year, it has become obvious that the challenges of operating, maintaining and enhancing the railway are significant," he said.
"I think it's time to level with the public and say that some of these extraordinary projects that we absolutely need are going to take longer and are going to cost more than we originally thought.
"We are going to take the summer to re-evaluate the extension of the programme - we need to do that properly with the Department for Transport and, of course, looking at the impact on trains as well."
He said it would not be possible to estimate the impact of the delays on the final cost.
Mr Carne said it was important to be honest with the travelling public: "Rather than beating ourselves up over some rather arbitrary target, I think we should level with people and reset expectations around what we can deliver.
"Our railway is a great success story, passenger numbers have doubled in the last 20 years - but it's a huge challenge to transform the performance of our railway while still providing a great service to the four-and-a-half million people that use our railway every day."
Satisfaction falling
The announcement comes as the latest rail passenger satisfaction survey is released.Travellers in London and south-east England are the least happy with their service, according to Transport Focus (formerly Passenger Focus).
The proportion of passengers satisfied has fallen from 82% last year to 80% this year.
Satisfaction on First Hull Trains was highest at 96%, while Southern was the lowest at 72%.
