A new international strategy to warn of virulent diseases before they take hold seems to have been activated too late in Mexico. Geoffrey Lean reports

International early-warning arrangements, designed to stop epidemics spreading, have comprehensively failed at their first test in the Mexican flu crisis, an Independent on Sunday investigation has established.

The newly established system is supposed to make it possible to stamp out an outbreak of a flu strain in the area where it first appears, but the virus had spread around the globe before the alarm was sounded nine days ago. The World Health Organisation (WHO), the Mexican government and other national health authorities seem to have been slow in picking up on what was taking place.

They swung rapidly and vigorously into action on 24 April when the WHO finally alerted the world to the danger of swine flu. But this was two and a half weeks after the first warning by local health authorities and a private international health surveillance firm, and more than a week after WHO had originally been notified.

Since the first days are all important in stifling an outbreak, the delay could prove to be extremely costly in human lives should the virus cause the deadly pandemic feared by many scientists. And even if it does not – as seemed more likely late last week – the breakdown of the system will lead to calls for urgent reform to enable the world to defuse future threats.

The WHO, which has named the flu A(H1N1), is already examining its response to the crisis. "We are documenting everything we have done, when we did it and how we have done it," a spokesman said on Friday.

The early-warning system is contained in new legally binding International Health Regulations – adopted by WHO's 193 member nations in 2005, and coming into force in June 2007 – which oblige governments to notify the organisation within 24 hours of an "unusual or unexpected" outbreak of flu, smallpox, polio or severe acute respiratory syndrome (Sars) which "may have serious public health impact". The WHO and the relevant government then have to decide within 48 hours if such an emergency exists and if so, to start taking measures to tackle it and prevent its spread.

The system was introduced after Chinese government secrecy held up attempts to control its 2002 outbreak of Sars which – although it spreads much more slowly than flu – infected 29 countries before being stamped out. But, while there is no suggestion of concealment by the Mexican government, the system still seems to have failed.

Nobody knows when A(H1N1) began infecting humans in Mexico. But documents seen by the IoS show that a US biosurveillance firm, Veratect – which monitors the internet for reports of disease worldwide – reported on 6 April that officials in Veracruz state had declared a "health alert" after recording 400 cases of illness among the 3,000 people of the village of La Gloria, where the first official case of the virus was later recorded.

Veratect says that an epidemiologist from the Pan American Health Organisation (Paho), which serves as the WHO's regional office, looked at its report on 10 and 11 April. The firm posted another warning on 16 April – the day that President Obama landed in Mexico on his official visit – indicating that the disease had spread to the state of Oaxaca. It says that its chief scientist, Dr James Wilson, was so alarmed that he twice sent the posting direct to WHO, on 16 and 17 April, followed by email on 21 April. Yet the official alarm was not sounded until three days later.

Dr Miguel Angel Lezana, director of Mexico's National Epidemiology Centre, said he notified Paho of the outbreak on 16 April. But the organisation countercharged that Mexico had failed to respond to its request to notify other nations. Neither Paho nor WHO responded when asked to comment. But wherever the true responsibility lies, the international system failed to pick up on a disease that it was supposed to cover until 18 days after a private firm had done so.

Part of the problem was that attention was focused elsewhere. For the past four years international bodies have been concentrating on H5N1, a particularly deadly strain of bird flu, spreading from Asia, that has been widely expected to be the cause of the next pandemic. Mexico was largely ignored, as swine flu has rarely spread to the human population.

Yet a very similar H1N1 strain has been found in US pigs since 1998, and has been rapidly evolving ever since, leading a senior US Department of Agriculture scientist to warn last year that it posed the "potential for pandemic influenza emergence in North America". And even at the height of concern about bird flu, leading scientists warned that the true threat could arise suddenly from a different source.

Scientists are now trying to work out why almost all the deaths have occurred in Mexico. Although the virus has spread to 16 countries, virtually every case elsewhere has proved to be mild. They have largely discarded explanations such as air pollution in Mexico City, its altitude, and a second, complicating, infection. The likeliest reason is that A(H1N1) is indeed a mild virus, killing a very low proportion of those it infects, but that hundreds of thousands have caught it in Mexico compared with only 650 elsewhere.

Experts warn, however, that it is too early to relax. The 1918 pandemic, which killed 50 million people, began as a mild virus, but returned as a fatal one four months later. They add that the world needs a crash programme to produce a vaccine against that eventuality.

Global killers: Four diseases that shook the world

1918: Spanish flu (H1N1) Ancestor of today's swine flu. It began as mild outbreak but returned four months later as a killer that claimed 50 million lives worldwide, more than perished in the whole of the First World War.

1968: Hong Kong Flu (H3N2) The cause of the last pandemic, and still part of the cocktail that gives us seasonal flu each winter. A comparatively mild virus: it killed just a million people.

1997: Bird Flu (H5N1) First emerged in Hong Kong, died away, then came back in South Asia. Particularly dangerous, has so far killed 60 per cent of the fewer than 500 infected. But not yet transmitted between people.

2002: SARS Severe acute respiratory syndrome (Sars) broke out in China. It was covered up by authorities and so spread around the world. Deadly, but not very infectious: around 8,000 fell ill of whom 774 died.