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Amnesty's claim surrounds two major oil spills at Bodo, Ogoniland in Nigeria, which the non-government organisation said Shell made false claims about to minimise its compensation payments.
Amnesty says its documents also reveal that Shell has known for years that its pipelines in the Niger Delta were old and faulty.
In 2011, Shell accepted full liability for two massive oil spills that devastated a Nigerian community of 69,000 people and could take up to 20 years go clean up.
The asset in question is a joint venture between state-owned Nigerian National Petroleum Corporation (55%), Shell Petroleum Development Company (SPDC, 30%) Total E&P Nigeria (10%) and Nigerian Agip Oil Company (5%), which carried out E&P in Ogoniland from the 1950s until 1993 when they stopped due to a rise in violence, threats to staff and attacks on facilities.
One of the Niger Delta's main pipelines - the active Trans-Niger Pipeline (TNP) - traverses Ogoniland.
The SPDC JV also has five non-producing fields and a network of about 100 wells and associated infrastructure in the region.
The area remained volatile after the JV withdrew, and oil and gas facilities continued to be targeted by saboteurs, oil thieves and illegal refiners.
Nigeria's government commissioned a SPDC JV-funded UN Environment Program (UNEP) report assessing Ogoniland as part of a wider reconciliation process in 2007, which was delivered in 2011.
The report identified 15 SPDC JV sites as needing further remediation. Shell said an inventory and physical verification of assets in Ogoniland has been completed and SPDC is working with its joint venture partners and the government to develop a decommissioning plan for the assets.
SPDC has also completed a comprehensive review of its remediation management system and made a number of improvements in line with best industry practice; while contractors have been re-trained on clean up and remediation techniques and SPDC has assigned specialist supervisors to a number of project sites to ensure effective oversight and compliance.
However, Amnesty wants more blood.
It says it had "irrefutable evidence" that Shell underestimated the Bodo spills emerged in a UK legal action brought by 15,000 people whose livelihoods were devastated by oil pollution in 2008.
Amnesty said the court action was what forced Shell to admit it has underplayed the true magnitude of at least two spills and the extent of damage caused.
"Amnesty International firmly believes Shell knew the Bodo data were wrong. If it did not it was scandalously negligent - we repeatedly gave them evidence showing they had dramatically underestimated the spills," Audrey Gaughran, director for global issues at Amnesty International, said.
"Shell has refused to engage with us and only now that they find themselves in a UK court have they been forced to come clean."
The court papers include an internal memo by Shell based on a 2002 study that states "the remaining life of most of the [Shell] Oil Trunklines is more or less non-existent or short, while some sections contain major risk and hazard".
In another internal document dated 10 December 2009 a Shell employee warns: "[the company] is corporately exposed as the pipelines in Ogoniland have not been maintained properly or integrity assessed for over 15 years".
"It's outrageous that Shell has continued to blame the vast majority of its spills on saboteurs while knowing full well how bad a state its pipelines were in," Gaughran said.
"After these revelations, the company stands completely discredited."
She said that while Shell's joint investigation report for the first oil spill in the Bodo area of the Niger Delta claimed only 1640 barrels of oil were spilt in total, an independent assessment published by US firm Accufacts calculated the total amount of oil spilt exceeded 100,000bbl - which Amnesty said Shell denied and repeatedly defended its far lower figure.
"In the court documents, Shell admitted its figure was wrong in both that case and a second spill, also in 2008, in the same area. The admission throws Shell's assessment of hundreds of other Nigeria spills into doubt, as all spill investigations are conducted in the same manner," Amnesty said.
"For years Shell has dictated the assessment of volume spilled and damage caused in spill investigation reports, now these reports aren't worth the paper they're written on.
"These spill investigation reports have cheated whole communities out of proper compensation."
She said the "Joint Investigation Visit" reports decide whether a community gets any compensation and the amount they receive. They also determine the extent of the clean-up required.
While the people of Bodo have been able to take legal action in the UK, Amnesty says the vast majority of the hundreds of thousands of people in the Niger Delta who suffer oil spills from Shell's operations will never have this opportunity to challenge the oil giant.
"Pollution from Shell's operations has wrecked people's homes, farms and fishing waters - their ability to send their children to school and put food on the table," Gaughran said.
She said Shell's admission makes clear the Joint Investigation Visit forms - which record the cause of the spills in addition to the volume and impact - could not be used as "credible sources of information".
"Shell will no doubt continue to defend its abysmal record in Nigeria by more misdirection, blaming spills on oil thieves. But the basis for these claims are the Joint Investigation Visit forms - which Shell must now admit are entirely unreliable," Gaughran said.