Transport Secretary Chris Grayling wants each rail franchise to be run by joint management teams, including representatives from both the
train operating company and Network Rail.
Mr Grayling said: "I intend to start bringing back together the operation of track and train on our railways."
The changes will start when each franchise is renewed in the future.
The minister said he wanted the changes to improve services for passengers, who are travelling on an increasingly crowded and expensive network.
"We need to change the relationship between the tracks and the trains on the railway," Mr Grayling said.
"In my experience passengers don't understand the division between the two.
"They just want someone to be in charge. They want their train to work. I agree with them," he added.
Each franchise will be run by one joint team, but the franchise owners and Network Rail will continue to exist separately.
The first new joint management teams will come into operation when the South Eastern and the East Midlands franchises are re-let in 2018.
The rail privatisation project was initiated in 1993 by John Major's Conservative government.
The old state-owned British Rail was broken up, and the ownership of the UK's rail infrastructure was separated from the control of the trains and services running on it.
This separation is held by some critics to be a significant source of delays to management decisions, repairs and train services.
Network Rail, which runs the UK rail infrastructure, was reclassified as a public sector body in September 2014.
Network Rail's chief executive, Mark Carne, said he welcomed the new plan "to bring more joined up working within the industry"
But Mick Cash, general secretary of the RMT rail union, told the BBC the new move was "a slippery slope to privatisation and the break-up of Network Rail" and that the union was "deeply concerned".
"We don't want to go back to the Railtrack days," he said. "It's quite clear they want to break up Network Rail, they want to privatise the rail infrastructure.
"We don't want to go back to the days of [rail disasters] Hatfield and Potters Bar - that's what happens when you get the private sector in charge of our infrastructure."
Shadow transport secretary Andy McDonald told the BBC the government "appears to be contemplating is yet further complexity, yet further fragmentation, and more opportunities for private entities to extract value out of our railway system".
He said that franchises should be brought back under public ownership as they come to be renewed.
However, Mr Grayling said the changes were "not about privatising Network Rail, it's not about handing over control of the track to train operating companies, it's about forging partnership alliances between the two".
They are already trying something like it across Scotland and with South West Trains.
As for getting one private company running everything on a future Cambridge to Oxford line, some fear it's an attempt to privatise rail repairs, which ended disastrously under Railtrack.
Speaking to the transport secretary, though, he told me that he had no intention of making radical changes across the network, or breaking up Network Rail. He just wants the public and private sector, train and tracks, to work together - not against - each other.
The new management approach may also be applied to the running of the revived "Varsity Line" between Oxford and Cambridge.
The recent Autumn Statement confirmed that the line, which was closed in the 1960s, should be rebuilt and reopened.
The line will be designed, constructed and run by a new body called East West Rail, which will be separate from Network Rail.
Mr Grayling said that, on this line, the track would be publically owned but run by a private company, and would "provide a degree of comparison with Network Rail to say 'can we build lines quicker and cheaper than we are at the moment?'."
Do you think this is a good idea or will we have a situation where it is unclear as to who is resposible for what?
Tuesday Dec 6, 2016