Soon the Great British Olympic moment will be over. The closing ceremony will be held this weekend and this year's Paralympics will be finished by early September. By the turn of the season the magic will finally have faded. The nature of the legacy left in its wake, for London in general and the people of Newham in particular, remains to be decided ( NB: some locals have already complained about being short-changed.)

Many will be sad to see this grand sporting pageant disappear, particularly because London 2012 has, so far, been a stunning success. From the impressive opening ceremony to the outstanding performances of our athletes (the best for a century), the show has gone extraordinarily well, exceeding expectations. Despite the cock-ups with G4S, no major security issue has surfaced yet and looks unlikely to. Even the weather behaved itself. The whole event seems on course, without indulging in overstatement, to go down as a landmark moment in modern British history.

Yet, despite the charm and coruscation of the games as a celebration of international talent (embodied in the epic performances of Jessica Ennis, Mo Farrah and Chris Hoy among so many others), there's a darker side to London 2012.

Not long ago, the International Olympic Committee (IOC) accepted the controversial American Chemical Company Dow as a "worldwide Olympic partner" to the games. This, despite Dow being known for its role in producing the chemical defoliants that allegedly devastated the lives of Vietnamese soldiers and civilians during the war with the United States. Prior to the lighting of the Olympic torch in Greece this spring, the Vietnamese government wrote a letter to the IOC, expressing the "profound concerns of the Government and people of Vietnam about the decision of IOC to accept the Dow Chemical Company as a global partner sponsoring the Olympic Movement."

To this day, innumerable Vietnamese and American victims are believed to be suffering from the effects of "Agent Orange", the herbicide produced by Dow and used for the purpose of destroying local crops and cover for the Vietcong. It was also allegedly intended to drive civilians from rural areas. In Vietnam alone, an estimated three million people are believed to be physically afflicted because of the defoliant, with grave health risks passing from those who were first exposed to succeeding generations.

The substance contained Dioxin, one of the most noxious chemical pollutants known to man. It is conservatively considered as toxic as nerve gas. Dioxin is recognised as both a leading carcinogen and a cause of horrific birth defects.

Unsurprisingly, deaths from cancer and, even now, an otherwise inexplicable excess of terribly deformed infants are occurring in large numbers in the East Asian nation. The government of Vietnam estimates that at least 150,000 children have been born with birth defects as a result of the use of Agent Orange by the US .

Two damning studies show massive amounts of Dioxin in areas that were heavily exposed to the herbicide. In one case, samples taken from a former US airbase in Danang showed dioxin levels 300 to 400 times higher than healthy limits. The study also concluded that rainwater had carried dioxin into urban drains and local communities, endangering 100,000 people. This is only one example in a single area- the US are believed to have dropped 80 Million Litres of Agent Orange on Vietnam and surrounding countries including Laos and Cambodia.

In the second case, Dr Arnold Schecter, an expert in Dioxin contamination found that soil samples taken in Bien Hoa, beside another former airbase, indicated that Dioxin levels were 180 times above the limits deemed acceptable by the US environmental protection agency. Washington knows of these studies.

A case made by Vietnamese victims of Agent Orange was dismissed by an American court in 2005.

Dow remains a hugely successful company. In the manner of many other corporate gargantuans, it fully bought up a rival chemical firm, Union Carbide Corporation, as a subsidiary in 2001. Union Carbide were responsible in the 1980s for one of the world's worst industrial disasters, which killed up to an estimated 25,000 victims affected by a devastating leak from the plant. The catastrophe also damaged the health of hundreds of thousands of others.

This year, Amnesty International wrote damningly of Union Carbide's response to the incident: "[the company] walked away from Bhopal without cleaning up, without disclosing the exact nature of the gas that leaked from its plant, and without paying adequate compensation to the victims."

According to reports, contaminants from the site appear to be still risking the health of the people of Bhopal. In 2009, the BBC took a water sample from a pump in "constant use" to the north of the site and found that it had "1,000 times the World Health Organization's recommended maximum amount of carbon tetrachloride, a pollutant known to cause cancer and liver damage." Dow has resisted pressure to further address the suffering of the people of Bhopal despite some elaborate attempts by activists to draw attention to the problem. It did, however, pay for "Stratfor", a private intelligence firm, to investigate campaigners seeking compensation for the victims, apparently indicative of the values that underpin the company's financial success.

Besides partnering with Dow, Olympic organisers initially approved a visiting Sri Lankan delegation to attend the games, echoing the decision to allow a similar congregation including President Mahinda Rajapaksa at the Queen's Jubilee celebrations. The same goes for the Bahraini Royal family who preside over a government troubled by serious allegations of human rights abuses (Nasser bin Hamad Al Khalifa is the head of the Bahraini Olympic Committee- he was in attendance at the opening ceremony). Shouldn't the Queen- moreover, the British government- have made a stand by dispensing with expedients and sending a strong message about human rights by refusing to host such people? In the end Rajapaksa's visit was cancelled, for reasons that seem unclear.

In 1962 the IOC took the brave step of expelling South Africa from the Olympics, in accordance with the principles echoed in the charter of the Olympic movement as it reads today. Nothing so courageous or honourable has been demonstrated 50 years later, despite the committee being spoilt for choice in terms of participating nations at London 2012 whose governments are ripe for censure.

Speaking on the presence of the Sri Lankan team, a protester named Praveen told me "I am very proud that we have the most prestigious sports event of the world at our doorstep." "However", he added "I raise the question as to why [representatives of a nation governed by] a violent racist regime [are] allowed to participate in something which promotes diversity, equality and fair play?"

Angry questions can equally be raised over the IOC decision to "partner" with sponsors that gain perceived endorsement from the Olympic movement in return for their money. In the case of Dow, millions of people are believed to have been affected by Agent Orange and the Bhopal disaster. Their suffering endures, even as Dow's profits continue to pour in, its yearly revenues regularly amounting to Billions of dollars.

Dow appears to be willing to spend big on Olympic advertising, but has resisted calls to re-engage with Vietnamese and Indian campaigners. Surely, the $100 Million that Reuters reports Dow forked out for a ten-year Olympic advertising deal in 2010 would have been better used as aid for the families of children with deformities, or in cleaning up a plant that is still, in all probability, damaging the health of thousands of Indians? Sadly, it seems, in the world of corporate and political realpolitik such magnanimity is considered wildly inexpedient.

Whereas Dow can resort to their lawyers to avoid alleged liabilities for the pain in Asia they are credibly linked to, the IOC and British organisers did have a choice about which partners to associate with. Their decisions in that regard taint this otherwise triumphant event and constitute an offence against the spirit of the Olympic movement of which they are supposed to be the faithful custodians.

Cheer the Olympics, but shame on the IOC.

Follow Emanuel Stoakes on Twitter: www.twitter.com/@EmanuelStoakes