There is a diplomatic disaster brewing between the United States and Indonesia after Indonesia's military chief was stopped from boarding a plane for the US.

Key points: Indonesian military chief General Gatot Nurmantyo was invited to the US for an anti-terror conference

Indonesian military chief General Gatot Nurmantyo was invited to the US for an anti-terror conference His ban from the US is a suspected bureaucratic stuff-up

His ban from the US is a suspected bureaucratic stuff-up General Gatot previously criticised presence of US marines in Darwin

The controversial and oft-offended General Gatot Nurmantyo has demanded an explanation from the United States.

General Gatot had been invited to Washington DC by his US counterpart— Chairman of the Joint Chiefs of Staff General Joseph Dunford — to attend an anti-terror conference.

He is a regular visitor and had the right visa —but as he and his wife were checking in for their Emirates flight to Washington on Saturday night, they were given bad news.

Indonesia's military spokesman Major General Wuryanto said "before departure, there was a notice from the airline that the military commander and his wife are not allowed to enter the US by the order of US Customs and Border Protection".

There has been no explanation yet from the United States, other than a statement from the Embassy in Jakarta apologising for the inconvenience to General Gatot, and saying it was prepared to facilitate his travel.

But that may not be enough for General Gatot.

"The military commander and his spouse and the delegation decided not to fulfil the invitation of the US military commander until there is formal explanation from the United States," Major General Wuryanto said.

Unlike some other Indonesian military leaders, General Gatot is not accused of any human rights abuses — there is no obvious reason to ban him from going to the US.

The Lowy Institute's Aaron Connolly suspects a bureaucratic stuff-up.

"A number of Indonesian military officers have been told they will not be allowed entry to US, and have been denied visas, but there has never been a situation to my knowledge where an Indonesian military officer has been granted a valid visa to enter the United States and then been denied entry prior to boarding the aircraft," he said.

"This is highly unusual and seems to me the most likely explanation was there was an administrative snafu that Customs and Border Protection should have informed Emirates that the General was allowed to board the plane and they didn't do that."

Military chief has criticised Australia

General Gatot is deeply suspicious of the US and Australia.

Earlier this year he criticised the presence of US marines in Darwin and he stunned Australian politicians and military leaders when he suspended military cooperation with Australia over allegedly offensive course materials at a Perth SAS barracks.

Army commander Angus Campbell came to Indonesia to apologise personally.

Australian Army commander Angus Campbell shakes hands with General Gatot Nurmantyo. ( Supplied: Indonesia Armed Forces )

In General Gatot's most recent controversy, he ordered the entire Indonesian military to watch screenings of a notorious anti-communist propaganda film.

The film is part of an effort to whitewash the military's role in the massacre of half-a-million so-called communists in 1965 and 1966.

Mr Connolly said General Gatot may use this latest incident to his advantage.

"Given Gatot's history, this is someone who has made a political reputation of identifying phantom threats to Indonesia's sovereignty and pride, so it's in his interest to publicise this as much as possible and to maximise the offence that Indonesians will take from this," he said.

The General is due to retire next year and his supporters are urging him to run for president in 2019.