The palm oil magnates are growing ever more trees for use in biofuels and carbon trading. But what happens to the subsistence farmers who live on the lucrative land?

Honduras and the dirty war fuelled by the west's drive for clean energy

The west's drive to reduce its carbon footprint cheaply is fuelling a dirty war in Honduras, where US-backed security forces are implicated in the murder, disappearance and intimidation of peasant farmers involved in land disputes with local palm oil magnates.

More than 100 people have been killed in the past four years, many assassinated by death squads operating with near impunity in the heavily militarised Bajo Aguán region, where 8,000 Honduran troops are deployed, according to activists.

Farmers' leader Antonio Martínez, 28, is the latest victim of this conflict. His corpse was discovered, strangled, in November.

Peasant farmers say they are the victims of a campaign of terror by the police, army and private security guards working for palm oil companies since a coup in June 2009 ended land negotiations instigated by the deposed president, Manuel Zelaya.

Witnesses have implicated Honduran special forces and the 15th Battalion, which receives training and material support from the US, in dozens of human rights violations around the plantations of Bajo Aguán.

They say private security guards regularly patrol and train with the soldiers, and have even been given military uniforms and weapons for some operations.

The military denies the allegations, blaming the United Peasant Movement (Muca) for escalating violence in the region. Repeated requests for comment from the US embassy in Honduras failed to elicit a response.

Land occupations

The Bajo Aguán dispute dates back almost 20 years, to a World Bank-funded land modernisation programme. The farmers say thousands of hectares of land used for subsistence farming were fraudulently and coercively transferred to agribusinesses that grow African palms, which are lucratively exported to the west for biofuel, and are traded in the carbon credit market.

Since then, they have tried to reclaim the land using the courts, as well as roadblocks and illegal land occupations.

Zelaya launched an investigation to resolve the conflicts, but this came to an abrupt halt when he was toppled in a coup in 2009 that was backed by the business, political, military and church elites.

In December 2009, groups of subsistence farmers started large-scale illegal occupations on disputed land also claimed by the country's biggest palm oil producer, the Dinant Corporation, which is owned by Miguel Facussé, one of Honduras's most powerful men.

Dinant says 17 of its security guards were killed and 30 injured in clashes with farmers.

The region was heavily militarised in early 2010, and the farmers who were occupying the land were forcibly removed by soldiers enforcing contentious court orders. Accusations of human rights violations have escalated ever since.

In one incident, in 2012, Neptaly Esquivel, 32, a father of five, was permanently disabled by a bullet to the hip fired at close range by a soldier, whose face was hidden by a balaclava, during a peaceful protest against education reform. His case is with the inter-American court of human rights.

In another incident, Matías Vallé, 51, a founder member of Muca, was shot dead by two masked men on a motorcycle as he waited for a bus. Witnesses said a car full of private security guards was parked a few metres away.

His wife, Dominga Ramos, said he had rejected money from Dinant employees to stop the farmers' movement, after which he was told there was a price on his head.

Ramos said: "I witnessed one police officer trying to hide a bullet shell in the ground with his foot. We buried him in a secret place so they couldn't remove his head. I am tired and scared.

"My two sons left because of threats. We just want to work our land in peace."

Dinant strongly denies any direct or indirect involvement in death squads or human rights violations.

It denies collusion between its security guards and government security forces to target peasant groups, and says it is committed to corporate social responsibility. The company says government security forces have been deployed against trespassers, who Dinant says are guilty of murder and other crimes.

A spokesman said Dinant was "not familiar" with the cases of Martínez, Esquivel or Vallé, and it had never been investigated for any suspected involvement. The company said it remained committed to "a quick and peaceful resolution to the Aguán conflict".

Another recent case is the disappearance of Josbin Santamaría Caballero, who was allegedly shot and taken away in an army helicopter on 30 October 2013 as his wife and two young daughters cowered in their kitchen of their home.

The Dinant spokesman said the company was ignorant of his case, too.

Caballero, 25, son of a prominent peasant activist, had been publicly denounced as a violent criminal by Colonel German Alfaro, commander of the joint police-military Xatruch operation in the region.

Alfaro, trained at the Western Hemisphere Institute for Security Cooperation (formerly the School of the Americas) in Fort Benning, Georgia, denied any military involvement and said Muca, the most organised peasant group in the region, was responsible for the current violence.

Alfaro said: "Muca and other groups encourage farmers to confront agro-industrialists, maintain constant tension and insecurity, and commit crimes to destabilise the area with armed groups."

Wider struggle

The Aguán conflict mirrors a wider struggle over land and natural resources across Honduras that for decades has pitted the poor majority against the country's 10 oligarch families. Honduras became the world's most violent country outside a war zone in 2011, and it is one of the poorest and most unequal in the Americas.

Activists say the use of state security forces to suppress protests against landgrabs, dams, mining and oil concessions has intensified since the 2009 coup. Over the same period the US has built up its military presence, with several bases in the country, which has become a major transit point for the international drugs trade. Between 140 and 300 tonnes of cocaine are believed to pass through Honduras every year en route from South America to the US and beyond.

Elections late last year boosted the status quo when the rightwing National party returned to power on a pro-business, pro-security manifesto amid allegations of electoral fraud and voter intimidation.

Bertha Oliva, director of the Committee of the Relatives of the Detained and Disappeared, said: "The police and military are using the cover of the US-led war on drugs in Honduras to eliminate many people, maybe including me: I am on the death list again."

An investigation published in February by the Canadian group Rights Action (pdf) detailed 34 acts of violence and other crimes directly implicating the 15th Battalion. It said these typically occurred "in co-ordination with private security forces of palm oil corporations, Honduran national police agents and other military units … in what can only be characterised as death-squad activity."

Karen Spring, from Rights Action, said: "The role of the military in terrorising and criminalising communities in the Bajo Aguán shows the complicity of the Honduran state and US government in supporting big business regardless of the killings."

The use of private security has increased exponentially across Honduras, which now has five private security guards to every police officer.

The UN working group on mercenaries described consistent reports of guards using illegal weapons to carry out with impunity human rights violations including killings, disappearances, forced evictions and sexual violence.

Patricia Arias, who led the UN group, told the Guardian: "The most worrying information is about private security guards acting together with the police and army, for example the Xatruch operations in Bajo Aguán."

Héctor Castro, vice-president of the Federation of Palm Growers, said both sides had committed abuses and broken the law. He added: "We don't have a government or authorities which look for conciliation or apply the law equally."

Vitalino Alvarez, a Muca leader who survived an assassination attempt in November 2012, said: "Each threat, disappearance and murder is part of the campaign of terror against us. We are blamed for killing each other and publicly called assassins, drug traffickers and drunks. We live, work and negotiate with guns pointed to our heads."

From bananas to biofuels

Honduras was the original, archetypal banana republic: a small, poor, fertile country controlled by a small group of wealthy families with ties to transnational business interests such as Chiquita, formerly the United Fruit Company.

Bajo Aguán, with its lush terrain, sunny climate and myriad rivers, was once dominated by banana trees. In this landscape, poor campesinos barely scraped a living from back-breaking work.

Banana companies withdrew from the region in the 1930s, and its population declined. But by the 1980s the Aguán was one of the most diverse crop regions in Honduras, producing coconuts, pineapples, grapefruits and almost half of all the country's bananas.

But African palm plantations have increased by almost 50% in the past three years, and now dominate the Bajo Aguán landscape, having replaced bananas and other edible crops. African palms, the saturated oil of which is a staple ingredient in processed foods and biodiesel, are now the most profitable crop in Honduras.

• This article was amended on Tuesday 6 January 2014. Josbin Santamaría Caballer was allegedly shot and taken away on 30 October 2013, not 2012 as we said. This has been corrected.