A three-year investigation by the United Nations will almost entirely exonerate Royal Dutch Shell for 40 years of oil pollution in the Niger delta, causing outrage among communities who have long campaigned to force the multinational to clean up its spills and pay compensation.

The $10m (£6.5m) investigation by the UN environment programme (UNEP), paid for by Shell, will say that only 10% of oil pollution in Ogoniland has been caused by equipment failures and company negligence, and concludes that the rest has come from local people illegally stealing oil and sabotaging company pipelines.

The shock disclosure was made by Mike Cowing, the head of a UN team of 100 people who have been studying environmental damage in the region.

Cowing said that the 300 known oil spills in the Ogoniland region of the delta caused massive damage, but added that 90% of the spills had been caused by "bunkering" gangs trying to steal oil.

His comments, in a briefing in Geneva last week, have caused deep offence among the families of Ken Saro-Wiwa and the eight other Ogoni leaders who were hanged by the Nigerian government in 1995 after a peaceful uprising against Shell's pollution.

With 606 oil fields, the Niger delta supplies 8.2% of the crude oil imported by the US. Life expectancy in its rural communities, half of which have no access to clean water, has fallen to little more than 40 over the past two generations.

Communities accept that bunkering has become rife in some areas of Ogoniland, but say this is a recent development and most of the historical pollution has been caused by Shell operations.

Last year, Amnesty calculated that the equivalent of at least 9m barrels of oil has been spilled in the delta over the past half a century, nearly twice as much as the 5m barrels unleashed in the Gulf of Mexico by the Deepwater Horizon disaster.

Tonight the investigation was accused of bias by Nigerians and environmental groups who said the study – paid for by Shell and commissioned by the Nigerian government, who both have massive oil interests in the region – was unbalanced.

Ben Ikari, an Ogoni activist, said: "Nobody from Ogoniland would be surprised, because the federal government of Nigeria and Shell are the same cabal that killed Ken Saro-Wiwa and others."

Ben Amunwa of London-based oil watchdog group Platform said: "The UNEP study relies on bogus figures from Shell and incomplete government records. Many Ogoni suspect that the report's focus on sabotage and bunkering will be used to justify military repression notorious in the Niger delta, where non-violent activists, including Ken Saro-Wiwa, were executed."

Cowing defended the UN report. In a series of emails seen by the Guardian, he said: "UNEP is not responsible for allocating responsibility for the number of spills being found in Ogoniland. Rather, we are focusing on the science. The figures referred to are those of the ministry of the environment and the department of petroleum resources.

"This is a Nigerian issue, not a UNEP issue. However, I would add that from our extensive field work throughout Ogoniland we have witnessed, on a daily basis, very large scale bunkering operations.

"It's very controversial. We cannot say whether a particular spill is from one cause or another. Our observation is that there is a serious [bunkering ] problem. I am being seen to be siding with the oil companies, but I am not.

"We were provided with the official spill site list. This is given by the oil companies themselves but is endorsed by the [government] agencies. We are not on the side of the oil companies."

He denied the UN was being influenced by Shell or the government. "We believe that it is correct that Shell [Nigeria] fund the study, as this is in compliance with the internationally accepted norm of the 'polluter pays'. No party … will be able to influence the science."

The full report, due to be published by December, is expected to warn of an environmental catastrophe.

"This is not directly comparable to the spills that occurred in the Gulf [of Mexico]," said Cowing. "But we have a serious and profound problem."

Tonight, environmental groups expressed shock at the report. Nnimmo Bassey, chair of Friends the Earth International and director of Environmental Rights Action, Nigeria's leading environment group, said: "It is incredible that the UN says that 90% is caused by communities. The UNEP assessment is being paid for by Shell. Their conclusions may be tailored to satisfy their client. We monitor spills regularly and our observation is the direct opposite of what UNEP is planning to report."

A June 2009 report by Amnesty International called the damage in the delta a "human rights tragedy", and blamed the government and oil firms, mainly Shell, for years of pollution. It recognised that oil bunkering had caused spills, but said "the scale of this problem is not clear".

The UN report saw more than 1,000 soil and water tests and other investigations carried out, and hundreds of communities consulted. The data generated is the first step towards a massive clean-up.

Oil production in the delta started during the 1950s, but was suspended in the 90s due to unrest. The oil fields in Ogoniland have since remained dormant.

• This article was amended on 23 August 2010. The Niger delta supplies 8.2%, not 40%, of the crude oil imported by the US. This has been corrected.