In Britain, it would pass unnoticed; to the Japanese, it is nothing short of the collapse of civil society. As of next week, the trains in Tokyo may be running a few minutes late.

East Japan Railway (JR East), the privatised company that until now has given Tokyo the world's most efficient and punctual public transport system, has been caught red-handed stealing water from a river many hundreds of miles from the Japanese capital and using it in its hydroelectric plants, the power behind the glory of a rail system that is the envy of the rest of the world.

As a consequence, it is in a desperate and wholly unfamiliar scramble to find the electricity it needs to run the service to the impeccable standards that everyone has come to expect. The prospects of securing that power appear bleak and, in terms that send a chill along station platforms across the capital, JR East said that it “cannot rule out the possibility that train operations will be affected”. Moreover, it has done little to dispel the appearance of panic. “We are walking a tightrope securing the energy we need,” Satoshi Seino, the company's president, said last week.

The looming disaster (by Japanese standards, if not of those glumly trekking through London Waterloo each morning) may be an indignity too far for a country that has been buffeted by the most violent recessionary nosedive in living memory. Over the past six months, the Japanese have watched as stock markets have imploded, property prices crashed and GDP contracted at a pace that has startled even the most bearish of economists. And through it all, they have been able to cling to perhaps Japan's proudest achievement: a metropolitan rail network that seamlessly carried millions of blue and white-collar workers into and around the city every day.

The trains are clean, fast and frequent. The drivers mentally divide their working days into 20-second segments to ensure that the system runs smoothly. You could, it was said, set your clock by the time of your train into town.

But for the past seven years, it seems, JR East's spectacular record of efficiency has been built on a combination of fraud and resource theft that has centred on the Shinanogawa River in the northern prefecture of Niigata, where JR East has a hydroelectric plant that supplies about a quarter of the power to the Tokyo rail network.

The plant was supplied with water through the sluices of the Miyanaka Dam, which in turn were controlled by JR East. The local government believed that it was able to control the railway's exploitation of the river by installing gauges that measured daily water intake and limited usage to 317 tonnes per second.

According to the Ministry of Transport, JR East tweaked the gauges by installing a piece of software that set them to read the magic number of 317 when far more water was passing through them. Hundreds of millions of tonnes of water are believed to have been stolen between 2002 and 2008, a period in which JR East was able to boast of punctuality records that were impressive even by its own astonishing standards.

Downstream of the Miyanaka Dam, meanwhile, a once-mighty torrent was reduced to an anaemic trickle and local fishermen despaired of their dwindling salmon catch.

JR East's warnings of trouble looming on the line follow the Transport Ministry's decision to revoke the company's permit to draw water from the Shinanogawa River, depriving the rail network of the 450 megawatts of electricity that the plant produced.

Under normal circumstances, the extra power might have been easy to source from thermal or nuclear plants elsewhere, but Tokyo already has significant generating problems. Tokyo Electric Power is scrambling to meet demand after the closure in 2006 of its Kashiwazaki nuclear plant because of a powerful earthquake.

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