Shell has never denied that its oil operations have polluted large areas of the Niger Delta – land and air. But it had resisted charges of complicity in human rights abuses.

Court documents now reveal that in the 1990s Shell routinely worked with Nigeria's military and mobile police to suppress resistance to its oil activities, often from activists in Ogoniland, in the delta region.

Confidential memos, faxes, witness statements and other documents, released in 2009, show the company regularly paid the military to stop the peaceful protest movement against the pollution, even helping to plan raids on villages suspected of opposing the company.

According to Ogoni activists, several thousand people were killed in the 1990s and many more fled that wave of terror that took place in the 1990s.

In 2009, in a New York federal court, that evidence never saw light during the trial. Shell had been accused of collaborating with the state in the execution in 1995 of writer Ken Saro-Wiwa and other leaders of the Ogoni tribe. Instead, Shell paid $15.5m (£9.6m) to the eight families in settlement.

Among the documents was a 1994 letter from Shell agreeing to pay a unit of the Nigerian army to retrieve a truck, an action that left one Ogoni man dead and two wounded. Shell said it was making the payment "as a show of gratitude and motivation for a sustained favourable disposition in future assignments".

Brian Anderson, the director of Shell Nigeria during those years, said in 2009, after the New York settlement, the company had "played no part in any military operations against the Ogoni people, or any other communities in the Niger Delta, and we have never been approached for financial or logistical support for any action".

But he conceded that Shell had paid the military on two occasions.

The company has been sued many times over its conduct in Nigeria. Amnesty International and Human Rights Watch (HRW) say oil companies working in the delta, of which Shell is the largest, have overseen a "human rights tragedy". Most of the alleged human rights abuses, they say, follow the companies' refusal to abide by acceptable environmental standards.

Despite the flood of lawsuits, cases can be delayed for years. Very few people are able to take on the oil giant, which has 90 oil fields in the delta where it has operated since the 1950s.

Increasingly, though, international groups are using courts in Europe and the US against big oil companies. Shell's Nigerian subsidiary SPDC admitted liability last month in a British court for two oil spills in 2008 around Bodo, which has severely affected the lives of 69,000 people. The company is negotiating a settlement. A similar case is being heard in a Netherlands court for three other spills.

In 2009, Amnesty international said oil companies in Nigeria had fostered a "human rights tragedy" with continual oil spills, gas flaring and waste dumping. "The people of the Niger Delta have seen their human rights constantly abused by oil companies that their government cannot or will not hold to account," said Audrey Gaughran, the group's global issues director.

HRW investigators visited the Niger Delta in 1997. Their report, in 1999, said: "People are brutalised for attempting to raise grievances with the companies; in some cases security forces threatened, beat, and jailed members of community delegations even before they presented their cases."