New trains due to be introduced later this year will not be able to run properly because the network doesn't have enough power.
It could be three years before the electrical supply is upgraded to enable the new trains to operate to their full potential.
Sussex train operators South Central, Connex South Eastern and South West Trains are spending millions on new trains which are air-conditioned, have greater acceleration and more room.
The trains will be introduced during the next few years, with the first batch due to arrive from manufacturers Bombardier and to have trials on the Brighton Line later this year.
However, little consideration has been given to providing the extra power.
The Bombardier 375 trains have sophisticated air conditioning and sliding doors, which use more power.
Without the extra juice they will not be able to run at full speed and the air-conditioning may not be able to be switched on.
It could mean they will have to run as four or eight car trains, defeating the object of reducing over crowding.
As some of the new trains have 15 carriages instead of the 12 on the existing units, some station platforms would have to be extended.
Railtrack, which is responsible for ensuring the appropriate power gets to the track and the platforms are long enough, is behind with its power enhancement and station upgrade programme.
It will be at least three years before the programme is completed.
A spokeswoman for South Central said: "We have the new trains on order and we hope to see the first ones introduced on the Brighton Line later this year.
"We are working with Railtrack to try to resolve the situation about the power and station improvements."
Michael Holden, southern regional director for Railtrack, said: "We are looking at a substantial upgrade programme, which has not been defined. It will take us more than three years to do, even if we do get the funding.
"We have lost a year or so. I don't think any of us realised how near the limit of the power supply we were operating."
He added: "I am very pleased with the progress made in the last month with creating a cross industry approach to addressing the power supply challenge."
Shelley Atlas, chairman of Brighton Line Commuters, said: "Railtrack should explain why it will take three years to upgrade the supply.
"I can't understand why this has not been thought of earlier. Commuters will be demanding explanations."
Lewes MP Norman Baker, who commutes by train to the Commons, said: "It is just another example of how privatisation has not worked. One sector working separately to another means commuters have to suffer."
The Strategic Rail Authority, which oversees the rail system, has met with the rail companies and manufacturers Bombadier and hopes improvements can be made by 2004.
SRA chairman Richard Bowker said: "Everyone involved recognises the need to adopt a holistic approach to ensure that the introduction of new trains on the network is achieved over the next two years.
"This new SRA-led industry group is fully focused on identifying and delivering whatever improvements are deemed necessary to bring about a smooth transition, in line with the phasing out of the slam door stock by the end of 2004."
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