The lives of thousands of young Central Americans are in danger after a rescue programme targeting victims of gang violence was suspended under Donald Trump’s sweeping refugee ban.

The Central American Minors (CAM) in-country refugee processing scheme was halted after the US president’s executive order froze the US refugee admissions programme for 120 days, ostensibly to beef up security checks.

CAM was launched by the Obama administration at the end of 2014 amid growing concern that children fleeing escalating violence in El Salvador, Honduras, and Guatemala were being forced to risk the treacherous journey through Mexico in order to seek refuge at the US border.

Criminal gangs, corrupt security forces and widespread impunity have fuelled rampant violence in the region, known as the Northern Triangle, where 33,000 people have been murdered in the past two years.

After Syria, whose armed conflict has triggered the worst humanitarian crisis since the second world war, the three countries are now the most deadly in the world.

Those affected by last week’s executive order include teenagers threatened with death after witnessing gang killings and others fleeing forced recruitment by crime factions. Most are virtual prisoners inside their homes, having abandoned school and work as a result of the threats and beatings.

“Every extra day that passes is another day that these youngsters have managed to stay alive. The situation is very dramatic. Some are so scared to go out that they’re not getting enough sunlight,” said Vinicio Sandoval of GMIES, a group working with the victims in San Salvador.

Trump has frequently berated Mexico for what he says is a failure to crack down on immigration, but he has so far failed to mention Central America, the starting point for most migrants who reach the southern US border.

The unfolding humanitarian disaster in Central America has forcibly displaced hundreds of thousands of people in the past few years, but has failed to attract anything like the global attention given to the refugee crisis in Europe.

A surge in unaccompanied children, especially young teenagers fleeing dangers such as forced gang recruitment, sexual slavery and extrajudicial killings, at the US border was described as a humanitarian crisis by Barack Obama in June 2014.

The response was largely punitive: millions of dollars were funnelled to Mexico to fund efforts to detain and deport Central Americans before they could reach the US. Almost 80,000 children have been detained by Mexican immigration agents in the past two years; another 100,000 have survived people traffickers, corrupt officials and kidnappers to make it to the US border.

Amid criticism from human rights groups, CAM was introduced to provide a safe way for selected victims under 21 to enter the country and reunify them with parents already legally resident in the US.

In 2014, a Guatemalan migrant, Gladys Chinoy, 14, waited after a freight train suffered a minor derailment, leaving her stranded for more than 12 hours in a remote wooded area in Mexico. Photograph: Rebecca Blackwell/AP

So far, 1,800 people have been allowed into the US as refugees or parolees – a lower level of protection – including some infants.

The vast majority are from El Salvador, where murder rates have surged to civil war levels in the past two years. In 2014 and 2015, at least 60,000 children left the country or dropped out of school because of violence, according to education ministry figures. El Salvador has a population of six million.

The refugee ban means as many as 9,000 youngsters whose CAM applications are currently under consideration, or who have been accepted but are awaiting permission to travel to the US, now find themselves in legal limbo.

Trump’s blanket ban triggered widespread condemnation, with protests erupting in cities across the world. As well as singling out seven mainly Muslim countries, Trump’s far-reaching directive also cut by more than half the annual cap of refugees to be accepted by the US, from 110,000 to 50,000.

Yet activists say refugees seeking asylum in the US are already subject to stringent security assessments.

“Entering the US as a refugee is the most difficult way of entering this country – the process can take up to 36 months and [already] involves screenings from 12 to 15 agencies including the Department of Homeland Security, the Department of Defense and CIA,” said Jennifer Sime, head of US programmes at the International Rescue Committee, which helps resettle refugees.

Once the programme reopens, there could be further delays depending on what additional security clearances are imposed.

Wendy Young, president of Kind (Kids in Need of Defense), which works with unaccompanied child migrants and refugees in the US, said: “These children need our protection. They are fleeing from horrific gang and narco-related violence which their governments cannot control. They’re not a terrorism risk, and the irony is that they’re already the most vetted of all migrants.”