For more than half a century the displaced people of the Chagos Islands have sought to return to their home, a collection of coral reefs in the Indian Ocean that constitutes one of the more far-flung outposts of the British empire.

But, despite interminable legal proceedings, their efforts have so far come to nothing, partly because studies commissioned by the UK government have concluded that a resettlement programme on what is officially known as the British Indian Ocean Territory was just not feasible.

As a result, today the only people who inhabit the 60 or so islands that lie halfway between Tanzania and Indonesia are the thousands of US military personnel based on its largest atoll, Diego Garcia, which, under an agreement with Britain, has been transformed into a huge landing strip used by B-52 bombers and anonymous jets moving high value terrorist detainees to CIA black sites around the world. But now the officially sanctioned arguments made against allowing the Chagossians to return to the islands from which they were removed in the late 1960s have been thrown into question.

A former British high commissioner has questioned whether the Foreign Office tried to “massage” the drafting of a key study that put paid to any hope of returning by concluding that resettlement was financially “prohibitive” and too “precarious”.

David Snoxell, who was deputy commissioner for the BIOT between 1995 and 1997 and later became high commissioner to Mauritius, made the claim after it emerged the Foreign Office had paid an academic to critique the original draft of a 2002 study that was considerably more positive about the prospect of the Chagossians making a successful return to their homeland than the final published version.

Documents released under the Freedom of Information Act show that the Foreign Office approached Charles Sheppard, now a professor of life sciences at Warwick University, to “review in confidence” the 850-page original draft of the study.

The release of the documents comes at a crucial time. The supreme court is considering claims that the original draft was not disclosed in 2008 when the House of Lords rejected an earlier appeal by the Chagossian people to return home.

It is argued that sharing the contents of the original draft of the study with the Lords “would have been highly likely to have affected the outcome of the appeal”.

The study, conducted by an independent consultancy, Posford Haskoning, was written in 2002, in the aftermath of the 9/11 attacks, when the US was opposed to sharing the atoll with the Chagossians.

The FOI documents show that Foreign Office officials were concerned about its findings. In an email sent on 24 April 2002, Charles Hamilton, the Foreign Office official in charge of the Chagos Islands, approached Sheppard saying: “I need to talk to you at some convenient time about the draft of the feasibility study which I have now received.”

Hamilton explained: “I need someone to review in strictest confidence the draft to check whether the science is sufficiently robust to support its conclusions. If we are going to base future policy on the study we need to be sure of this in our own minds. Would you be prepared to do this for me against payment of an appropriate fee?”

Sheppard accepted the brief, telling Hamilton in a later email that he believed his brief was to ensure that the Foreign Office had “a scientifically bulletproof” report.

But it was clear that the decision to draft in Sheppard to critique the report alarmed the consultancy. On 18 June Hamilton emailed Sheppard saying no fewer than six employees from Posford Haskoning would be at a meeting to discuss his recommendations – and those of another consultant brought in by the Foreign Office – as to how the report should be changed.

Snoxell told the Observer that he had been unaware of how closely the Foreign Office had been involved in shaping the final version of the 2002 study, key sections of which arguing against the case for return are now considered by some academics to be scientifically flawed. “I understood at the time that it was to be an entirely independent study into the feasibility of resettlement,” Snoxell said. “So these email exchanges surprise me as they look rather incriminating. It appears they were trying to massage the draft of the feasibility study, which the FCO has always claimed was an independent study by consultant experts.”

This interpretation was rejected by Sheppard, who insisted that all parties were aware of his involvement and that the study’s terms of reference made clear the original draft would be subject to scrutiny by the Foreign Office. “I was paid to comment on the science, which I did,” he said. “If government, indeed anyone, are going to draw important conclusions, I think their evidence should indeed be ‘bulletproof’, and I said so.”

A spokeswoman for the Foreign Office said: “There was no undue influence by FCO officials on the analysis contained in the 2002 feasibility study. The documents simply illustrate the assurance process the government undertook in ensuring the independent advice it relied upon in the formation of policy was scientifically robust.”

The UK must decide by 29 December as to whether the US-UK agreement over the use of Diego Garcia as a military base should be extended for 20 years.

It has been argued that few Chagossians want to return to their homeland. But a government report, published last week, suggests that 98% of them want the right to go back. Chagossians have expressed a desire to develop a sustainable economy on the islands. One avenue for exploration is high value tourism. Another is fishing – although conservation groups fear what this could mean for the islands’ abundant marine life.