The deep bullet wound in Hilda Lezama's thigh is a livid pointer toHonduras's unwanted status as the latest front line in America's war on drugs.

For all of her 53 years Lezama has lived in Ahuas, a village of wooden homes built on stilts, close to the fast-flowing Patuca river in the remote Mosquitia region of eastern Honduras. For 25 years, her family have run a business ferrying locals up and down the waterways that link the isolated jungle settlements.

On such a trip two months ago, she was shot from an American helicopter in a counter-narcotics raid involving US drug enforcement agents and Honduran troops. Four other local people, including two women, were killed.

"We were returning from a trip downriver with the fishermen," she remembered. "We were travelling at night to avoid the heat. We heard the helicopters above us, but we couldn't see them. They could have let us dock and then searched the boat, but instead they shot us. Maybe they were thinking we were someone else."

US officials say Lezama's boat had picked up a stash of drugs flown into an airstrip close to the river, a charge she categorically denies. "If we were criminals we could not complain, but we are innocent working people," she insisted.

The Americans say none of their agents opened fire. According to the US ambassador in Honduras, Lisa Kubiske, a preliminary investigation by the Honduran authorities "suggests there was no wrongdoing" by the security officials. That proposition may be tested in the Honduran courts. A human rights group, the Committee of the Relatives of the Disappeared (Cofadeh), has filed a legal complaint against the Honduran and US governments citing violations of human rights.

The Ahuas raid was no isolated incident. Within the last month agents from the US drug enforcement administration (DEA) have shot dead two suspected traffickers in raids in eastern Honduras.

The increasingly aggressive anti-trafficking strategy – codenamed Operation Anvil – is aimed at intercepting illegal drugs flown into the sparsely populated Mosquitia region from South America. More than 80% of the cocaine entering the United States is now thought to be transshipped through Honduras.

The US has long had a military presence at the Palmerola base in central Honduras, but what was once a key asset in the war against the Sandinistas in neighbouring Nicaragua is now focused on the war on drugs.

Honduras has granted the Americans access to three "forward operating bases" in remote areas frequented by the traffickers. DEA agents have been embedded with the Honduran security forces and the operation is supported by six state department helicopters, piloted by non-US security contractors not bound by strict rules of engagement for US service members.

According to Kubiske the new strategy is working: "More than 100 planes came into the country last year with drugs. Now interdictions of drug operations happen on a regular basis … Death or injuries are not the norm."

That is of little comfort to Lezama. She was sent home from hospital when she ran out of money. Heavily bandaged and unable to walk, she scoffs at the US ambassador's talk of a thorough investigation of the Ahuas raid. US officials have not contacted the victims, she said. "My son-in-law was killed, two of my neighbours were killed, and I was wounded, so where are the Americans? Don't you think they should talk to me?"

The Honduran government insists its efforts to combat the traffickers will continue, and so will co-operation with the Americans. Officials point to evidence suggesting Mexican cartels have moved significant resources and manpower into Honduras as a result of the military crackdown on their operations in Mexico.

"Every day, the narco-traffickers are innovating how they work, and changing what they do," said Colonel Ronald Rivera Amador, in charge of Honduran military operations along the Mosquito Coast. "If we place obstacles in the way of their aircraft, they look for other routes, by sea or by land. They have communications, navigation and night-vision equipment that is better than ours."

In the Mosquitia region, long-neglected by the Honduran government, cocaine offers an unrivalled opportunity to make money. But the vast sums are having a corrosive effect throughout Honduras. As the trafficking has risen so have levels of violence, and Honduras now has the world's highest per capita murder rate. Its dominant criminal gangs – Barrio 18 and MS 13 – have forged alliances with some of Latin America's biggest narco-trafficking cartels.

Marlon, 27, was a member of the MS 13 until this year, when he tried to leave the criminal underworld behind. He was shot six times by his own crew, and left for dead. Now he lives in a safe house run by a Honduran charity, and asked only to be identified with a pseudonym.

Acccording to Marlon, MS 13 works closely with the Zetas, one of Mexico's most ruthless cartels. "We were like their servants," he said. "The money was in the millions."

The key to the traffickers' success was corruption, said Marlon. "Always, always, always when drugs are being moved, a member of the military is involved," he said. "They allow police officers to intercept a certain amount of drugs while the other part, majority is coming in through another channel. The police take a minimal amount, just to make it look as if they are doing a good job. Narco-trafficking has taken control of our country, it's everywhere, in politics, even in the churches."

The government has acknowledged that thousands of police officers have ties to organised crime. Officials say they are in the early stages of a purge: lie detector tests and drug-testing are to become mandatory throughout the force.

But the criminal networks are fighting back. The last chief of Honduras's anti-narcotics directorate was assassinated. The man tipped to succeed him was gunned down this year.

Following Mexico's example, the Honduran president, Porfirio Lobo, hasordered the military to join the crackdown on organised crime, and the country's latest anti-drug tsar, Colonel Isaac Santos, was drafted in from the army.

"The narco-traffickers have a huge capacity to corrupt, both forces and individuals," Santos said. "In reality, they have a lot of power. But the government cannot allow Honduras to become a narco-state, with a narco-government and a narco-police force. A terrible war is being fought in Honduras – a war which may affect the destiny of humanity. And as long as there is one honest person we must keep on fighting."

*Stephen Sackur's reports from Honduras will be on BBC HARDtalk and the 10 O'Clock News this week

Honduras's troubled history

It is hardly surprising that Honduras's political institutions have failed to stem the tide of violence and corruption sweeping the country: Honduran democracy itself was undermined by a military coup on 28 June 2009, which ousted the populist president Manuel Zelaya.

The generals forced Zelaya to flee to Costa Rica after he announced plans for a referendum on constitutional reform that could have enabled him to run for a second presidential term. The intervention of the armed forcesevoked bitter memories of two decades of military rule until the 1980s.

Latin American states condemned the coup. So – rather belatedly – did the Obama administration. But within months the US backed a new presidential election, and offered a warm welcome to the winner, Florida-educated conservative Porfirio Lobo.

His administration promised sweeping reforms, but has been dogged by allegations of human rights abuses.

According to the Honduran human rights group COFADEH, more than 300 civil society campaigners have been murdered since the coup. The figure includes trade unionists, campesino farmers demanding the restoration of lands acquired by Honduras's biggest landowners, gay rights activists, and more than 20 journalists.

When Alfredo Villatoro, one of the country's best-known radio journalists, was abducted and murdered two months ago, tens of thousands of protesters took to the streets of Honduras's towns and cities declaring "Killing journalists will not kill the truth."

As with the vast majority of the more than 6,000 murders a year recorded in this country of 8 million, the Villatoro case remains unresolved.

There is abundant evidence that elements within the police have been committing, not solving, murders. In the most notorious case, serving police officers were found to have killed the son of Julieta Castellano, the rector of one of Honduras's leading universities.

According to Marvin Ponce, vice-president of the Honduran congress, up to 40% of police have ties to organised crime. For all the talk of a clean-up, Lobo's choice of police chief, Juan Carlos Bonilla – more widely known as El Tigre – whose career has been dogged by repeated, though unproven, claims that he was a member of a police death squad more than a decade ago.

Last year 94 members of the US Congress called on the secretary of state, Hillary Clinton, to end all financial and logistical support for the Honduran security forces, "given the credible allegations of widespread, serious violations of human rights".

But US support for the Honduran government has in fact been boosted; a clear indication that Lobo is currently seen as a vital ally in seemingly never-ending war on drugs in Latin America.