An American environment group with strong links to the US government is privately opposing proposals by leading British environmental scientists for some of the exiled inhabitants of the Chagos islands in the Indian Ocean to be allowed to return home.

The islanders were ejected by Britain 40 years ago to make way for the giant US base at the Diego Garcia atoll. Last year, the British government announced the creation of the world's largest marine protected area round most of the Chagos islands – with the likely exception of Diego Garcia.

Chagossian exiles denounced the move as an attempt to pre-empt their hopes of a return – a charge the British government denies.

Evidently stung, some scientists who have researched the often pristine environment around the 55 Chagos islands say Britain should establish a research base that could employ up to 100 Chagossians and house their families. They made public their compromise plans, drawn up with groups representing the Chagossians, at a public meeting on the future of the Chagos islands held yesterday at the Royal Geographical Society in London.

However, email correspondence seen by the Guardian in the run-up to the conference reveals bitter divisions over the plan. Some members of the Chagos Environment Network (CEN), a group of environmental organisations formed three years ago to lobby for the creation of the protected area, are vehemently opposed to any Chagossian return.

Members of the CEN include British environmental NGOs such as the RSPB and the Marine Conservation Society, along with the Chagos Conservation Trust – a little known group long dominated by former British diplomats and soldiers – and the Pew Charitable Trusts, an influential US philanthropic organisation. The Pew Trusts organised and helped pay for one of the last acts of President George W Bush – declaring the Mariana trench in the Pacific Ocean a national monument, despite protests from local island leaders.

Dr Mark Spalding, a Cambridge University researcher who also works for the Nature Conservancy, said in the email correspondence that some members of CEN have "endorsed the concept of limited numbers of Chagossians living in the northern atolls to work on conservation and scientific monitoring", including "allowing settlement of families".

David Snoxell, a former British high commissioner in Mauritius and an active member of the Chagos Conservation Trust, said the plan for a Chagossian-staffed base "offers an imaginative way out of the current logjam".

But both Alistair Gammell, who recently left the RSPB to represent Pew in the UK, and Jay Nelson, director of Pew's Global Ocean Legacy project, reacted angrily. Gammell said "CEN has reached no such conclusion." Nelson said: "I know for a fact not all groups would agree."

Some of the scientists behind the compromise plan for Chagos believe they face an alliance between environmental hardliners and the military to keep the Chagossians far from their homeland – and to sideline them from the debate about the islands' future.

In the emails, Spalding said: "I have found it difficult to swallow that some of the conservation community have chosen to gloss over the impact of the military base." Snoxell complained that the CEN frequently "fails in [its] public relations material to mention the Chagossians".

The row between the environment groups was not mentioned at the London meeting, at which the scientists met some 150 angry UK-based Chagossian exiles. Most of the 5,000 or so exiles live in Mauritius and the Seychelles, where they were left by British naval warships between 1968 and 1972.

Britain asserts sovereignty over the Chagos islands, coral reefs and ocean – an area around the size of France, which it calls the British Indian Ocean Territories. The government says the creation of the marine protected area is "without prejudice" to future court rulings on the rights of the Chagossians. But Wikileaks recently published diplomatic correspondence in which a British official said it "put paid" to any future resettlement.

At the London meeting, Philippe Sands, a lawyer representing the Mauritius government in a legal action to reclaim the islands from Britain, accused environmental groups such as Pew of "aiding and abetting an illegal act" by the British government.