The Mexican government is struggling to re-establish order in the western state of Michoacán, after its offensive to disarm vigilante militias in the epicentre of the country’s drug war led to fatal clashes.

Members of so-called “self-defence” groups, which sprang up last year in parts of Mexico to fight drug cartels and took control of municipalities in Michoacán, met state and federal officials for talks amid an uneasy calm following the arrival of hundreds of federal police and troops.

But a pharmacy near the town hall in Apatzingán, one of the most volatile parts of the state, was torched early on Wednesday. The attack underscored a stand-off in which some militias were still holding on to their weapons, but agreeing not to flaunt them or to advance on any further municipalities. It occurred close to the city centre where federal police staged a display of force this week aimed at demonstrating that they were in control.

A spiralling security mess in a country where as many as 80,000 people are believed to have died during the unsuccessful war on drugs of President Enrique Peña Nieto’s predecessor, Felipe Calderón, is bad news as Mexico seeks to attract billions of dollars in investment to its newly liberalised energy sector.

It is also dreadful timing: Mexico is preparing to host Barack Obama, US president, and Stephen Harper, Canadian prime minister, for a trade summit next month.

At least one person was confirmed dead in clashes as security forces moved in, but the state ombudsman’s office said two were killed and unconfirmed reports put the number as high as 12, including a child.

The self-defence militias have been fighting to wrest back control of parts of Michoacán from the Knights Templar cartel, which nets an estimated $75m a year from extortion, money laundering and protection money. This is in addition to its profits from drug smuggling. It has also successfully branched out into controlling exports of iron ore to China, officials say.

Late last year, the Templars effectively took over Michoacán’s Lázaro Cárdenas port – an important Pacific entry to drugs and precursor chemicals as well as an exit for Michoacán’s iron ore, avocado and lime exports – taxing all merchandise. In what security experts saw as a brazen show of strength, they also attacked electricity installations, knocking out power to nearly half a million people.

That prompted the federal government to send in extra troops to support local authorities. But in a change of tack this week, Mr Peña Nieto sent a fresh wave of federal forces to take over security in the state and reimpose the rule of law – leading to fears that the authorities had lost their grip on what NGOs and a local bishop have described as a “failed state”.

“The government is taking decisive measure to re-establish order and the rule of law,” Luis Videgaray, the finance minister, told reporters.

The federal forces are disarming local police, many of whom are suspected of close links with organised crime, and the militias. Only last week, Miguel Angel Osorio Chong, the interior minister, was defending government protection for one prominent self-defence militia leader, Juan Manuel Mireles, saying that he had been “hurting” the Knights Templar.

But trying to use the vigilantes to fight a proxy war with the Templars was a strategy fraught with risk, threatening an escalation of the conflict, said Alejandro Hope, a security analyst, who noted the self-defence groups enjoyed popular support.

He said the government’s decision to take control “comes a year too late . . . you are going to have to use far more force than six or eight months ago, and these guys are not going to give up their weapons . . . They would be pretty much risking their lives if they did”.

The government’s response smacks of panic, Mr Hope added. “The problem is, the government is refusing to define this as an armed conflict, which looks terrible internationally, but that’s pretty much what we have here,” he said.

Soldiers and police were helping the six states bordering Michoacán tighten security to prevent any spillover of violence.

José Miguel Vivanco, Americas director of advocacy group Human Rights Watch, called the government’s response “improvised . . . and quite reckless”. The group has criticised Mr Peña Nieto for what it sees as a continuation of “disastrous” policies.

“Now, apparently, they’re relying on brutal force,” Mr Vivanco said.

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