Juan, an evangelical pastor in San Salvador, was running an errand on a Saturday afternoon last month when he came across familiar yellow police tape blocking the road not far from his church. A young man had been murdered.

“The worry that came to my mind was, will I make it home today, will I see my daughter again?” Juan, whose name has been changed to protect his identity, said. “You could feel tension in the air, a fear that was drowning the city.”

That day, 62 people were killed in the small country of 6.5mn people. The killings shattered murder records and threatened to destroy President Nayib Bukele’s reputation for taming violence in one of the world’s most deadly nations.

Less than a week after the murder spree, Bukele declared a state of emergency and had his security forces round up more than 5,000 alleged gang members.

His harsh crackdown on gangs has led to a renewed confrontation with rights groups which say that it opens the door to abuses by security authorities in a country with a past history of rightwing death squads.

For decades, El Salvador has suffered high levels of violence from criminal gangs. Bukele made fixing it a top political priority after his election in 2019, and has claimed that his security policies are responsible for a fall in homicides. That decline began in 2016 but continued under his watch.

But the US government said his administration instead negotiated a secret truce with the gangs to lower violence in exchange for financial incentives and prison perks. In December, the US Treasury imposed sanctions on two Bukele administration officials, accusing them of holding the talks.

Bukele has denied negotiating with the gangs and called the US affirmations a “lie”.

Security analysts said the weekend’s uptick in murders showed how fragile those agreements can be.

“The gangs still have enough power to destabilise the country and Salvadoran society, that’s evident,” José Miguel Cruz director of research at Florida International University’s Kimberly Green Latin American and Caribbean Center.

Cruz believes the murders were a message from gangs trying to extract better terms from the government under its deal.

Over the past week in neighbourhoods known to have a gang presence, security forces set up checkpoints and raided houses, local media and witnesses said. Those detained were imprisoned and given reduced food rations of just beans and tortillas. Family members lined up outside detention centres trying to get information about loved ones.

“MESSAGE TO THE GANGS: We have 16,000 Homeboys [gang members] . . . we took everything from them, even their mattresses for sleeping, we rationed their food, and now they won’t see the sun,” Bukele tweeted.

The government has introduced draconian measures to crack down on the gangs, making it easier for authorities to tap phones, introducing 10-year jail terms for those as young as 12 years old simply for being gang members, and allowing 15 days of detention without a court hearing.

The surge in crime has added to mounting political problems for Bukele, an authoritarian populist who has burnt bridges with Washington after trampling on constitutional rights, and alarmed the IMF by adopting bitcoin as legal tender.

The adoption of the cryptocurrency has emerged as a roadblock to a deal with the IMF for a $1.3bn loan to help finance El Salvador’s budget and bring down the cost of its debt.

The president last month delayed a much-hyped bitcoin bond that some hoped could help plug the fiscal hole partly created by the lack of an IMF deal and the high premium demanded by bond markets to lend. It remains unclear whether investors are willing to fund the bitcoin-backed issue. El Salvador’s sovereign bonds are in junk territory, with investors worried about the country’s ability to pay.

Bukele has also alienated the US, a former ally, by firing five Supreme Court judges whose replacements opened the door for his re-election, which was banned under the constitution.

Before the latest spate of violence, Bukele had the highest approval rating among 11 Latin America leaders, according to CID Gallup polling. This was partly credited to his perceived success in calming the bloodshed since he took office in 2019.

Supporters saw him as the leader who tried to change the image of the small Central American nation from one of the most dangerous countries in the world to a forward-looking frontier for cryptocurrencies.

In 2015, homicide rates in El Salvador hit more than 100 per 100,000, one of the highest in the world. Since then, murders have fallen precipitously. Security analysts say agreements with the gangs have probably been one reason for the decline.

But in 2021, the homicide rate was still just under 18 per 100,000, almost 18 times the rate in England and Wales in 2020/21.

In some communities “everyone is shut inside their houses with a lot of fear”, said Rina Monti, director of human rights research at Salvadoran non-profit Cristosal. “There has always been complicity between police and the gangs, so at some point you can’t be certain if actions . . . are really police orders.”

Monti said her organisation had received 13 complaints related to the police raids so far, including a taxi driver missing after being detained by authorities and a construction worker beaten up by security forces.

“It’s pretty scary,” said one 27-year-old who lives in a gang-controlled neighbourhood in east San Salvador, speaking on condition of anonymity. “Because you live in a bad, dangerous neighbourhood you’re deemed suspicious.”

The state of emergency can only last 30 days and homicides are already back down to lower levels seen before the spike, but analysts worry that the crackdown could fuel gang recruitment in the long run.

“You just deepen . . . this perception that the state is an abuser,” said Tiziano Breda, Central America analyst at the International Crisis Group. “You keep on fuelling a stigma and a hatred that pushes in many cases people to join gangs.”

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