Rail passengers may have to pay a premium for travelling in the evening rush-hour as well as before 10am.
The introduction of smart cards will enable train companies to levy a "congestion charge" for morning and evening peak travel.
The cards, similar to the Oyster cards already used in London, will make it easier to squeeze more out of passengers who use the most popular services.
The proposal comes as ministers are expected to refuse permission to widen the tracks between Brighton and London, so more face being squeezed on to already overcrowded services.
The Association of Train Operating Companies floated a peak pricing system in 2005 to combat the rising number of train users.
But this is the first time the Department for Transport has made specific recommendation for tackling congestion on trains from Sussex to London.
The move is outlined in a new report which sets out Government proposals for rail services in the South. The proposals will help form the DfT's White Paper on the future of the railways to be published this summer.
Overcrowding already affects a fifth of Southern peak morning services and one in nine First Capital Connect services from Brighton, according to the latest figures.
In the next 20 years, passenger numbers are expected to rocket by 26 per cent in the region, pushing the number of journeys to and from Brighton station up by 2.6 million a year.
Sharon Hedges, Southern manager for rail watchdog Passenger Focus, said: "I would like to see an alternative approach where people are encouraged to travel at other times through incentives."
Shelley Atlas, of Brighton Line Commuters, said: "I would not want to see commuters penalised but it is fair for those travelling off-peak to pay less.
"What is being proposed is no different to what happens with air travel."
On track widening, the Southern Regional Planning Assessment for the railway says: "It would be extremely difficult to widen the suburban corridors to provide extra tracks, which affects the choice of options for accommodating future growth to both suburban and long distance destinations."
The report suggests that trains are lengthened so that 12-car peak-time Southern trains leave from Brighton and eight-car from East Grinstead.
A £3.5 billion Thameslink programme, if given the green light, would lead to 12-car First Capital Connect trains on the Brighton line calling at London Bridge in peak periods.
Running double-decker trains from Brighton to London Bridge is also being looked at.
The long-term plans for the services using the Brighton line include: Trains lengthened to 14 carriages New track and signalling systems introduced to pinch points at Victoria, London Bridge, Clapham Junction and south of East Croydon Chichester/Arundel services run via Horsham to the Dorking line, instead of via Gatwick Airport
Should evening rush-hour rail passengers pay a premium? Are commuters already paying enough to travel by train?
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