Mexican authorities tracked down and killed “El Mencho”, one of the world’s most wanted drug traffickers, by following a romantic partner to his safe house near a picturesque mountain town, the head of the country’s defence secretary has revealed.

In a press conference on Monday, authorities provided the first details about the operation that led to the death of the leader of Mexico’s most powerful organised crime group, the Jalisco New Generation Cartel.

The raid on Sunday prompted a surge of retaliatory violence by cartel gunmen, which all but shut down entire areas of western Mexico.

The 59-year-old cartel leader, whose real name is Nemesio Rubén Oseguera Cervantes, was fatally injured as the Mexican military attempted to capture him in the operation, which was supported by intelligence from Washington. The US has been pushing its southern neighbour to take more aggressive action against groups trafficking fentanyl, methamphetamine and cocaine.

Defence secretary, Ricardo Trevilla Trejo, said that El Mencho’s bodyguards opened fire on the military as it encircled the cabin in a wooded area outside the town of Tapalpa, about 80 miles south-west of Guadalajara.

The gunfire forced one helicopter into an emergency landing in an echo of a failed 2015 attempt to capture him in which his gunmen brought down a helicopter with a rocket-propelled grenade.

Fighting continued as El Mencho fled the cabin into a nearby forest, where he was wounded and captured. He died while being transferred for medical treatment in Mexico City.

Aside from El Mencho, seven of his men were killed in the firefight, while two soldiers were wounded. Rifles and grenade launchers were seized.

The operation immediately set off a wave of violence across Mexico, with cartel gunmen blocking almost 100 major roads, torching vehicles and lashing out at security forces, especially in the states of Jalisco and Michoacán.

Security minister, Omar García Harfuch, said that 25 members of the national guard were killed and 14 wounded in those clashes, along with 34 gunmen and one bystander. Another 70 people were arrested across the country.

Trevilla confirmed that Hugo César Macías Ureña, alias “El Tuli”, a close ally of El Mencho’s who coordinated the rash of violence after his death – and even offered a bounty for every dead soldier, was also killed in a confrontation.

By Monday, authorities reported having cleared all blockades across the country. “Mexico is at peace, calm, and we are working in all the states,” said Mexican president, Claudia Sheinbaum.

However, there were still reports of burning vehicles in Michoacán, and schools remained closed in many states as a precaution. Some airlines are yet to resume normal service to the cities of Guadalajara and Puerto Vallarta, both in Jalisco, which took the brunt of the cartel’s fury.

Stephen Woodman, a security analyst in Guadalajara, said the violence “kicked off pretty immediately” as news broke of the operation on Sunday morning.

“[These groups] have plans in place to coordinate quickly in the event of a major arrest, to cause the maximum amount of trouble,” he said. “It was quite overwhelming with reports coming in all over the place.”

The sense of panic was compounded by the amount of misinformation, some using AI-generated photos and footage, that swirled around social media. “You had to question everything,” he said.

As the chaos spread, the Jalisco governor, Pablo Lemus Navarro, urged the state’s 8 million citizens to stay at home and suspended public transport.

Woodman ventured out in the late afternoon, once the initial action seemed to have died down. “It was eerily quiet: everything shut, no traffic,” he said. “But there was a very strong smell of smoke in the air.”

It was an alarming reminder of the cartel’s capacity to instil fear and panic in Mexico’s second-largest city, which is scheduled to be one of the 2026 World Cup host cities.

Other video footage showed tourists on the beach as huge clouds of smoke rose into the skies above Puerto Vallarta, a popular resort city on the west coast known for its spectacular Pacific beaches. Most flights into the city were suspended and international airlines cancelled dozens of trips.

Authorities there had issued a public advisory to stay indoors, and routes to airports may be blocked, the UK Foreign Office said in a travel advisory on Monday. The US embassy in Mexico City also issued a security alert, urging citizens to “shelter in place” in affected regions.

While less internationally famous than the Sinaloa cartel of the now imprisoned Joaquín “El Chapo” Guzmán, the Jalisco group is a household name in Mexico, where it is infamous for its displays of ultraviolence and its massive weapon arsenal, which it has shown off in military parades.

The cartel, which was founded about 16 years ago, has also been accused of attempting to assassinate Mexican government officials – including García Harfuch, whose car was riddled with hundreds of bullets in an upmarket neighbourhood of Mexico City in 2020, wounding him and killing two of his bodyguards and a bystander.

Washington had offered a $15m (£11m) reward for his capture, and the White House confirmed that the US provided intelligence support to the operation. Senior US officials celebrated the killing, which follows months of pressure from Donald Trump over the influx of drugs and migrants across the 1,954-mile (3,145km) border between the two countries. The Trump administration has designated the Jalisco cartel as a “foreign terrorist organisation”, and the US president has even threatened direct military action against cartels that he has claimed “are running Mexico”.

Writing on X, Christopher Landau, the deputy secretary of state, called El Mencho “one of the bloodiest and most ruthless drug kingpins”. He posted: “This is a great development for Mexico, the US, Latin America, and the world.”

While the killing may relieve pressure on President Sheinbaum from Trump, it will also create a cartel power vacuum. Sheinbaum has previously criticised the discredited “war on drugs” strategy, in which military action often triggers major violence only for new cartel leaders to emerge.

Chris Dalby, an organised crime expert who has written a book about the Jalisco cartel, said one of the biggest questions now facing Mexico was who – if anyone – would fill the dead criminal’s boots.

“If no one can, if the CJNG finally splinters, you have four or five different lieutenants with the manpower, the weaponry and the criminal empires to build their own fiefdoms – and that could plunge Mexico into almost record levels of violence,” Dalby said.

Some sources have cited El Mencho’s stepson, Juan Carlos, as a possible successor with enough backing to hold the cartel together. “If [he] can unite the CJNG we may avoid that kind of civil war,” Dalby said, although he said he believed that was far from guaranteed.