Arrest warrants have been issued in El Salvador for three former leftwing guerrilla fighters wanted in connection with the execution of two American soldiers whose helicopter was shot down during the country’s 1979-1992 civil war.

The warrants are the first of their kind since a 1993 amnesty law guaranteeing impunity for civil war crimes was annulled a year ago. They were issued amid growing anger at the government’s reluctance to pursue perpetrators.

El Salvador’s civil war left about 80,000 people dead, 8,000 missing and a million displaced in a country the size of the US state of Massachusetts, according to a 1993 UN Truth Commission report.

The overwhelming majority of war crimes were attributed to the American-backed armed forces and paramilitaries who often targeted civilians they suspected of supporting leftwing rebels. Yet surprisingly, the first warrants issued since the amnesty was declared unconstitutional are for former guerrillas.

The US army helicopter was shot down by a Farabundo Martí National Liberation Front (FMLN) patrol in January 1991 in the San Miguel district in eastern El Salvador, as it was flying back to base in neighbouring Honduras.

The pilot, Daniel Scott, was killed in the crash, but two wounded soldiers – Lt Col David Pickett and Cpl Earnest Dawson – were shot dead after the guerrillas stole the cache of weapons onboard the helicopter, according to the Truth Commission.

During the proxy cold wars that the US fought in Central America in the 1980s and 90s, Honduras was used to provide military support to neighbouring dictatorships and host CIA-backed rebel armies fighting leftwing movements.

Ronald Reagan’s administration funnelled the equivalent of $1m a day to El Salvador’s military dictatorship despite evidence of death squads and civilian massacres. The conflict ended in 1992, but peace never came to El Salvador.

The ruling rightwing Arena party pushed through the amnesty law in 1993, a week after the UN report was published, guaranteeing impunity for perpetrators of war crimes. Since then, warring street gangs, transnational criminal groups and state security forces have helped make El Salvador the second-most deadly country in the world, after Syria.

Amid growing frustration among victims, the supreme court held a public hearing last week about the lack of progress in prosecutions.

The attorney general, Douglas Meléndez, told the court that there were just three prosecutors dedicated to dealing with 139 complaints of human rights violations committed during the civil conflict. At least 50 are needed to investigate the cases, but the government has not been forthcoming with resources, Meléndez said.

The FMLN, which became a legal political party as part of the 1992 peace deal, has been in power since 2009; the country’s current president, Salvador Sánchez Cerén of the FMLN, was a former guerrilla fighter. Both major parties support a new reconciliation law which would guarantee impunity or at least scrap jail time for numerous fighters-turned-politicians.

Since the amnesty was overturned, the investigation into the 1980 assassination of Archbishop Óscar Romero has been reopened, and some military officers have been summoned to testify in the case of the 1981 El Mozote massacre in which elite government soldiers were accused of killing of between 900 and 1,200 people, mostly women and children.

But both cases are advancing painfully slowly as the fight for justice is being driven by the victims and human rights lawyers, not the attorney general’s office, according to the commentator Tim Muth.