Anthropologists and indigenous leaders have warned that a Natural History Museum expedition to Paraguay could lead to "genocide" and are calling for it to be abandoned. They fear that the scientists and their teams of assistants are likely to make accidental contact with isolated indigenous groups in the remote region they are planning to visit and could pass on infectious diseases.

The 100-strong expedition is due to set off in the next few days for two of the remotest regions of the vast dry forest known as the Gran Chaco, which stretches over northern Paraguay, Bolivia and Argentina. The expedition organisers hope to find several hundred new species of plants and insects.

But the two sites where the British and Paraguayan teams of botanists, biologists and other scientists plan to stay in for up to a month are known to be home to groups of Ayoreo Indians. They live in voluntary isolation and reject and avoid all contact with Westerners, said Benno Glauser, director of leading indigenous peoples' protection group Iniciativa Amotocodie.

Glauser, with the backing of Ayoreo leaders who have left the forest in the last 20 years, has sent the museum more than 40 pieces of data showing the presence of isolated peoples in the Chovoreca and Cabrera Timane regions.

"According to our data, the expedition you plan constitutes beyond any doubt an extremely high risk for the integrity, safety and legal rights of life and self-determination of the isolated Ayoreo, as well as for the integrity and stability of their territories. There exists a considerable menace and risk also for the safety of the scientists taking part of the expedition, as well as the rest of expedition participants," says Glauser in a letter to the museum.

Until about 1950 it is estimated that around 5,000 Ayoreo lived in the Chaco forest as isolated hunter-gatherers without contact with the ranchers and religious groups who were given land by the Paraguayan government. Since then almost all have left the forest after being targeted by American missionaries. It is estimated that there are now only six or seven isolated groups numbering around 150 people in total. It is now the only place in South America outside the Amazon where uncontacted Indians still live.

Ayoreo leaders who have settled near the town of Filadelfia in northern Paraguay this week appealed to the president of Paraguay and the Natural History Museum to abandon the expedition, saying that their relatives were in grave danger.

"Both of these regions belong to the Ayoreo indigenous territory ... We know that our people still live in the forest and they don't want to leave it to join white civilisation."

He said there are at least three uncontacted groups in the area. "If this expedition goes ahead we will not be able to understand why you prefer to lose human lives just because the English scientists want to study plants and animals. There is too much risk: the people in the forest die frequently from catching white people's diseases – the get infected by being close. Because the white people leave their rubbish, their clothes, or other contaminated things. It's very serious. It's like a genocide," they said in a statement.

According to Survival International, an NGO that campaigns for the rights of tribal peoples, contact with any isolated Indians would be disastrous for either party. "Contact with isolated groups is invariably violent, sometimes fatal and always disastrous," said Jonathan Mazower, a spokesman. "It is highly likely that there are small groups of isolated Indians scattered throughout the Chaco. The only sensible thing to do is err on the side of caution because any accidental contact can be disastrous. This has happened before [in the Chaco]. On two previous occasions, in 1979 and 1986 expeditions were sent in by US missionaries to bring out Indians and people were killed on both occasions."

The expedition, one of the largest undertaken by the museum in more than 50 years, has taken several years to plan and is believed to be costing more than £300,000. It hopes to map and record species of thousands of plants and insects, which will then go to local Paraguayan museums. Until last month, the museum's website had claimed that the area the scientists will visit "has not been explored by human beings".

This created consternation in the Ayoreo communities. "Some people say they are going to places in which no human being has ever been. That means we Ayoreo are not human beings," said one of the leaders in a statement to the Guardian. "Our uncontacted brothers have the right to decide how they want to live – if they want to leave or not."

The Chaco, known as "green hell" is one of the least hospitable but most biologically diverse places on Earth. The barely populated expanse of almost impenetrable forest is twice the size of the UK, but home to at least 3,400 plant species, 500 bird species, 150 species of mammals, 120 species of reptiles, and 100 species of amphibians. Jaguars, pumas, giant anteaters and giant otters are common.

In a statement, the Natural History Museum said it had planned the expedition in conjunction with the Paraguayan government and would be working with Ayoreo Indians: "We recognise the importance of the concerns which have been taken into account during the planning of the expedition. They form part of the ongoing consultations that are still taking place with the Paraguayan authorities. The information and specimens collected on this trip will help scientists to understand for the first time the richness and diversity of the animals and plants in this remote region and the governments and conservation groups are able to use such information to better understand how to manage fragile habitats and protect them for future generations."

It continued: "We are delighted to be working with representatives of the indigenous people. This gives us a wonderful opportunity to combine traditionally acquired knowledge with scientifically acquired knowledge to our mutual benefit. As with all expeditions, the team is continually reviewing the situation. Our primary concern is for the welfare of the members of the expedition team and the people of the Dry Chaco region."

Uncontacted tribes around the world

There are around 100 remaining groups of isolated, or "uncontacted" people, including 40-67 in Brazil, 15-18 in Peru, 15-30 in Papua and others in Bolivia, Paraguay, Ecuador, Colombia, and the Andaman islands of India. As oil companies, loggers and farmers go deeper into the remotest forests, evidence of more groups is being discovered.

A few groups may have no idea of country or other languages and no one has come close to them. Some are the descendants of tribes contacted more than 100 years ago by colonists who fled deeper into the forest in fear of enslavement or decimation by disease. Others shun all contact with western civilisation but have a good idea of life outside the forest and may have machetes or other tools which they could have acquired from contact with other groups.

According to Survival International, these tribes all remain in isolation because they choose to, and because encounters with the outside world have brought them only violence, disease and murder.

Isolated tribes are the most vulnerable people on Earth, having no immunity to the diseases brought in by outsiders. Colds and flu can become killers, and 50-90% of tribe members commonly die from first contact with outsiders.

Epidemics of measles, smallpox, yellow fever, whooping cough, influenza and later malaria have all had devastating effects.

More than 20% of the Yanomami Indians of northern Brazil died in the 1980s and 90s when they came into contact with goldminers who brought in illnesses. Ninety per cent of Indians in the Javari valley in Amazonas state in Brazil, including six uncontacted tribes, suffered from malaria or hepatitis brought into the area in 2006.

The result, says Survival, is that entire cultures that have taken centuries to evolve can be being wiped out in days as disease invades a population.

Anthropologists now take precautions including wearing masks to avoid accidentally passing on diseases.