Never mind the industrial guerrilla war on the railways: the really big transport dilemmas for the government lie on the roads.

By the end of the year, almost all the independent studies commissioned by John Prescott into the UK's transport corridors will have landed on the desk of his battle-scarred successor as the minister in charge of transport, Stephen Byers. Most will paint a familiar picture of congested motorways and disgruntled drivers. And most will prescribe an anti-congestive therapy of improved public transport; extra road space; and road charges, to prevent the new space filling up with more drivers.

If the politicians stay true to form, they will deliver properly only on the extra roads. The Treasury and the private sector will baulk at the bill for greatly improving the rail infrastructure, and ministers will recoil from the political risk of a new charge on motorists. That, the experts say, could generate even worse problems in the future by encouraging even more people to make the lifestyle choice of long-distance commuting. Eventually, the new space for mega-motorways will jam up again, leaving the next generation of political leaders with ribbons of Britain resembling Los Angeles, with congested approach roads and congested rural roads, as well as congested motorways.

The studies now coming to fruition were devised by Prescott to buy time while his department was being starved of cash in Labour's first term. He asked regional teams - dominated by local government and business but peppered with environmentalists - to study congestion problems and to devise complex and innovative solutions involving cars, trains, trams, buses, walking, cycling, land use and (crucially) demand-restraint.

Now the chickens are coming home to roost. It is clear that some of the teams have been shocked by their research. The South and West Yorkshire study, for instance, found that more than half the commuters on one stretch of the M1 were making a daily round trip to work of more than 86 miles - far higher than previously believed.

The Prescott solution would have been to lure many of these commuters from their cars into sparkling new trains, while deterring the obdurate remainder with congestion charges for entering city centres. But the Yorkshire consultation document makes it plain that public transport alone cannot unlock the M1 jams.

The trouble, it explains, is that motorways provided free of charge by taxpayers for strategic interregional traffic have been seized by commuters who choose to live in rural or suburban surroundings but work many miles away. The trend has been exacerbated by changes in employment patterns that have made workers reluctant to move house for jobs that are possibly precarious. In two-earner households, the choice of home is often determined by the job of the partner responsible for childcare, allowing the other to take to the motorway in search of riches.

Long-distance commuters, in other words, do it because they can. And now so many of them are doing it that they want the government to solve the congestion they have created. Most of these travellers, however, seem unlikely to choose the buses and trains promoted by Prescott. A new map tracing a complex commuter web across Yorkshire reveals that fewer than 10 per cent of M1 commuters actually penetrate into the town centres where the rail stations lie. Public transport journeys from one peripheral site to another would entail several time-wasting changes. And every year, local councillors make matters worse by approving new business parks straddling the M1 that generate even more traffic.

The consultant heading the Yorkshire study, Denvil Coombe, told the Today programme that expanding the M1 would be the answer only if access to the new road space were restricted to deter future congestion - to buses or freight, say.

One possibility is to install traffic lights on slip roads so drivers must queue to gain access to the motorway. This practice (known as ramp metering) is common in the US, but casts long tails of traffic on to the secondary road network. It also has a perverse effect: if all drivers face an equal queue to get on to the motorway, the system disproportionately punishes the commuter with the shortest journey and so encourages people to live even further from the office.

The obvious solution, Coombe believes, is congestion charging across the whole road network to prevent canny drivers deserting tolled motorways and clogging up local roads. There could be one set of motorway tolls, then a new set of tolls as soon as the driver enters the urban fringe. (Firms should not be allowed to escape toll zones by fleeing to urban fringes and generating yet more journeys.) In this scenario, the Yorkshire M1 might even be left unwidened. In the short term, Coombe says, this would generate huge revenues for investment in public transport; in the long term, it would persuade people to live closer to work or to telecommute more. If they chose to drive long distances, they would pay an economic price for the congestion they generate. Research suggests that charges of 20p per rush-hour kilometre in towns and 2p per kilometre on the motorway would stem two-thirds of the projected traffic growth.

Two of the regional studies are ambivalent on congestion charging. The Cambridge team recommends motorway-style roads ringing the town, but diluted its charging proposals after opposition from local councillors (critics warn that traffic into Cambridge may increase by 30 per cent as a result). The East Midlands M1 team says ten lanes of motorway may be needed to accommodate commuters around Nottingham, but fears charging because it would divert traffic and discriminate against poorer drivers. But even this study concludes: "Can we build our way out of congestion? The answer seems to be no!"

Most of the other studies are more or less pro-charging, although politicians involved are often keen to ensure that the charges are not imposed during their term of office. The Birmingham-Manchester study says the M6 in Staffordshire should be expanded, but then tolled in the future. The separate West Midlands study wants to restrict the M6 through Birmingham to its current width and urges Birmingham and Wolverhampton to price roads soon, with wider pricing to follow. The south Scotland study is grappling with similar ideas as the team studies maps showing drivers commuting coast-to-coast from the west of Glasgow to the east of Edinburgh - though a few members consider this a matter of voter choice.

The M25 study is perhaps most contentious. The consultants say a new road slicing the suburbs of London would be politically impossible, while a new outer M25, proposed by some motoring groups, would simply encourage even longer commuting. Research for the M25 team shows that most commuters hop on to the motorway for just one or two junctions to ease their journey to work. There is a strong case for making them pay.

The recommendations of the studies will present a challenge not just for the government, but also the opposition, motoring organisations and the media. As commentators clamour for more investment in transport and the Chancellor is advised that roads are better value than railways, there will be a strong temptation for ministers to commit to building their way out of the problem.

But in the long-term interests of commuters, business and society, we need a grown-up debate to tussle with the paradox that it may be in motorists' interests to deny them the extra roads they think they want, and to charge them for what they now enjoy for free.

The problem may not be quite as prickly as some suggest - an RAC survey showed that around half of all drivers would be prepared to pay £1.50 to save 20 minutes on a two-hour journey. And the RAC is preparing a major study to examine the potential for shifting motoring taxes on to congestion charging.

Ministers' response to the regional studies will show whether they want a short-term palliative to traffic jams, or whether they are really committed to governing for the long term.

Roger Harrabin is environment correspondent for BBC Radio 4's Today programme