Roger Mitton, Washington – There are tremors of apprehension in the United States about a serious downturn in its relationship with Indonesia.

Matters came to a head on Wednesday when the US House of Representatives voted down funds for military education and training to Indonesia until the murder of two Americans in Papua last year is investigated properly. Congressmen believe Indonesian military elements were involved in the Papua atrocity and want the guilty parties punished.

They are standing firm on this matter, despite the desire of President George W. Bush's administration to restore the funding, which was cut off after the involvement of the Indonesian army in massacres in the former East Timor. The amount involved, about US$400,000, is relatively small, but Jakarta views it as symbolic of America's commitment to friendly relations.

As a result of the military funding impasse and other contentious issues, ties have hit a rocky patch despite efforts by the State Department to keep things on an even keel, with aid continuing in areas such as health and education.

"I would say it is pretty bad," said Mr Donald Emmerson, a senior fellow at the Institute for International Studies at Stanford University, who is regarded as the doyen of America's experts on Indonesia. "There are a number of on-going points of tension and potential flashpoints."

Mr Dana Dillon, a senior policy analyst at Washington's Heritage Foundation, agreed, listing the US problems with the Indonesians. "They don't support the war in Iraq. They did not support the invasion of Afghanistan. Their government has only taken half-hearted economic measures. There is the murder of two Americans in Papua. There is Indonesia's half-hearted support for the fight on terrorism – there is a whole lot of things," he said.

The US now regards Indonesia's belated entry into the fight against terrorism as having tapered off, without Jakarta robustly following through against Jemaah Islamiah and other such groups. But it is the apparent involvement of the Indonesian military in the killings of the two American teachers from an international school in West Papua last August that is currently the major irritant between the two nations.

A campaign by the widow of one of the victims has made a big impact on congressmen, who have let Mr Bush know that they will not approve military-related funding for Jakarta until this case is resolved properly.

As if that were not bad enough, the Indonesian military's massive crackdown on Aceh separatists is also upsetting the US. Most galling to the Americans has been the way Indonesia has openly modelled its Aceh strategy on the "shock and awe" technique used by the US in Iraq, even to the extent of using embedded journalists.

Although Washington has repeatedly made clear that it supports Indonesia's territorial integrity, it has not condemned the Aceh separatist group GAM in the way Jakarta would like. "The Indonesians would love the US to declare GAM a terrorist organisation, like the Abu Sayyaf, but the US has not done this," said Mr Emmerson. Not only that, but many in the US view the Indonesian military as being as bad as GAM.

Last week's furore over the intrusions of US F-18 jets into Indonesian airspace indicates how, given the current tense state of relations, a small incident may cause ties to plummet further.

The taut situation is expected to cause apprehension across South-east Asia. No one in Asean wants a crisis to develop between its largest member and the US.

"Asean would love to have much better US-Indonesia relations," said Mr Dillon. Unfortunately, it is not happening. Basically, he said: "Americans don't understand Indonesia and the Indonesians really don't understand the US."