He insisted the landmark reforms did not have any secret agenda to hike ticket prices.
However, pressed on the issue on BBC Radio 4’s Today programme, he said: “We might as well have a grown-up conversation about it.
“There is a balance between the fact that the taxpayer has plugged a hole of £12 billion during the coronavirus to keep our railway afloat and the fact that people who use the railway are already subsidised by the wider taxpaying public.
“Of course, any government in the future will have to weigh those things up.
“But today is about simplifying and in doing so making a system which is much more customer-focused.”
The prospect of higher fares, though, will be galling to many commuters, especially as so many trains were virtually empty during lockdown periods and are still far below previous levels.
Ministers are not expected to seek to recoup the £12 billion from the fare payer.
The reforms also aim to drive efficiency which if delivered can keep down fare rises.
However, Mr Shapps’ words suggested passengers could pay a greater share in future of the cost of the railways, rather than the taxpayer.
Big hikes in ticket prices, though, would risk discouraging rail use at a time when the Government is seeking to persuade more people to use trains.
‘Agree a long term plan for London’
Meanwhile, business chiefs in London called for the Transport Secretary and Mayor Sadiq Khan to swiftly agree a long-term plan for funding Transport for London.
Adam Tyndall, programme director for connectivity at London First, stressed that the rail reforms could be “transformative if the detail is right”.
He added: “The decision to base nationwide service contracts on a TfL-style system is a significant vote of confidence in how transport operates in London. With this Review published, the Government must now rapidly agree a long-term, sustainable, funding settlement for TfL itself.”
He also warned: “The limited reform of fares and ticketing is a missed opportunity. It leaves operators with one arm tied and passengers’ expectations unmet.
“To bring commuters back to public transport after the pandemic, it will be critical to move to a ticketing system with clarity, flexibility and cost-effectiveness at its core.”
However, Mr Shapps hailed the reshaping of the rail system which will see control of trains and track brought under a new public sector body named Great British Railways.
He said it would deliver trains running on time, though, he admitted that passengers would have to wait a while for such greater punctuality.
GBR will own and manage rail infrastructure, issue contracts to private firms to run trains, set most fares and timetables, and sell tickets.
It will absorb Network Rail in a bid to end the current “blame-game system” between train and track operations when disruption occurs.
Operators will be incentivised to run high-quality services and increase passenger numbers.
Great British Railways established in 2023
However, GBR is not expected to be established until 2023.
Some reforms will come in within weeks including flexible season tickets, offering savings on certain routes for people who travel to work two or three times a week.
These will go on sale on June 21 for use seven days later.
Mr Shapps told BBC Breakfast: “People will start to see the benefits straightaway but I can’t pretend that suddenly, instantly just because we changed the name, the trains will suddenly run on time.
“That is going to take time to happen because the structures will take new time to get into place.
“But there is a downpayment with the flexible season tickets, there is a better way of running our railways…Great British Railways will become a brand which is trusted and known and actually has some control over what is happening on the railway which is something that has been missing for a lot of years.”
The Williams-Shapps Plan for Rail has been published as a white paper.
It is based on the recommendations of a review of the industry carried out by former British Airways chief executive Keith Williams following the chaotic introduction of new timetables in May 2018.
The plan was initially due to be published in autumn 2019 but was delayed by the general election and the coronavirus pandemic.
Boris Johnson said: “I am a great believer in rail, but for too long passengers have not had the level of service they deserve.
“By creating Great British Railways, and investing in the future of the network, this Government will deliver a rail system the country can be proud of.”
Logo an ‘updated version of British Rail’s double arrow’
The GBR logo will be an updated version of British Rail’s double arrow.
Rail franchises were effectively ended when the Government took over the financial liabilities of operators in March 2020 to keep services running amid the collapse in demand caused by the coronavirus pandemic, at a cost of £10 billion.
The emergency agreements will be replaced by passenger service contracts, with GBR contracting private firms to operate trains.
This concession model is similar to the one used for London Overground and Docklands Light Railway services by Transport for London.
Mr Shapps said the new Great British Railways body will give the public a simplified system.
He stressed that during the 2018 timetable fiasco there was no “Fat Controller” in charge of the system, referencing the Thomas The Tank Engine stories.
He told Sky News that under the new system “there will be a single organisation selling you the tickets and running the timetable”.
Mr Williams said: “Our Plan is built around the passenger, with new contracts which prioritise excellent performance and better services, better value fares, and creating clear leadership and real accountability when things go wrong.”
Anthony Smith, chief executive of passenger watchdog Transport Focus, said: “Passengers will welcome this move towards a more accountable and joined-up railway.
“Ultimately what they will care about is whether rail is the best option for them – if it is reliable, efficient and good value.”
However, Manuel Cortes, general secretary of the Transport Salaried Staffs Association (TSSA), dismissed the plan as “papering over the cracks”.
He said: “A concessions-based model will still see passengers’ and taxpayer money leak out of our industry in the form of dividend payments for the greedy shareholders of the private operators who will hold them.”
Robert Nisbet, director of nations and regions for industry body the Rail Delivery Group, also said the reforms did not go far enough.
He told ITV’s Good Morning Britain: “We would much rather see the bonnet opened and the whole system be tinkered with so it really does benefit the passengers.
“Because it’s not just the people on the trains, it’s about the economic recovery of Britain.
“That’s what really matters, and if you get the railways right, that should help Britain as it comes out of the pandemic.”
Jim McMahon, shadow transport secretary, said: “Nearly three years after it was commissioned, this report raises more questions than it answers.
“With fare hikes, £1 billion cuts to Network Rail and broken promises to communities across the country, it’s yet another example of ministers talking a good game with very little substance underneath.”