The freeholds of nearly 2,500 stations are to be transferred to Railtrack from next April, and the majority will be leased to franchised train operators, Mr MacGregor told the Conservative Party conference in Blackpool.
In most cases, the Government believes the freeholds will be taken by the private companies operating train services on franchises.
However, as with airports, the operators of the leases will be allowed to pass on charges for the use of their stations, which are likely to be included in train fares.
Railtrack, which will take charge of the rail network after the privatisation of BR, will develop options for the largest stations, including the sale of very long leases, possibly up to 125 years.
The Department of Transport said the move would enable stations, from small-town platforms to London terminals, to be commercially developed by the leaseholders. The plans open the way for some stations to be used by competing private operators, and seek to ensure that minority competitors have access to platforms and destination boards.
The train operators will be expected to pay for the use of stations. 'Where a station is used and managed by a single passenger operator, he will meet his costs, including the rent for the lease of the station, and reflect the costs in his franchise bid.
'Where a station is used by more than one operator, or is managed by an independent operator, there will need to be a station access agreement between the parties. The charges included in that agreement will be regulated,' the department said.
Mr MacGregor told the conference: 'Too often under British Rail ownership, stations have been the Cinderellas of the system. These proposals are designed to bring in private-sector finance and expertise to exploit their development and commercial trading potential.'
The department believes the vast majority of Railtrack's stations will be managed by the franchised passenger operator who is either the sole user or dominant user of the station.
The leaseholder for the station will retain the rental income from trading activities, which the Government said would provide an incentive to maximise the development of the station.
Where there is an independent station operator, the dominant train operator will be responsible for ticket sales, platform operations control, train announcements and departure indicators, and cleaning and maintenance.
The department said: 'Where there is more than one train operator, the minority operator should be able to establish his own ticket office, if there is space; have his own window or windows within a single ticket office; or have his tickets sold by the station operator on payment of commission, which would be subject to the approval of the regulator.'
Tory party conference, page 8