In its first comments on what has been described in Indonesia as a "diplomatic scandal", the US department has said in a statement that General Gatot's office was warned there might be a delay due to "US security protocols."

He was denied boarding his Emirates flight but was then cleared to travel and rebooked on a later flight.

General Gatot then chose not to travel, the statement said.

The general also spoke for the first time on Tuesday, saying he would not travel to the US unless he was instructed to go by President Joko Widodo.

Moments before his plane was due to depart from Jakarta on Saturday, General Gatot was informed by airline Emirates that he had been denied entry to the United States by US Customs and Border Protection, despite having a visa.

No light is shed by the departmental statement on the mysterious US security protocols that prevented General Gatot from boarding the initial flight, even though he had been personally invited to attend a counter terrorism summit by his US counterpart, General Joseph Dunford.

The statement comes as US Defence Secretary James Mattis apologised to Indonesian Defence Minister Ryamizard Ryacudu over the incident ahead of a meeting at the ASEAN Defense Ministers' Meeting in the Philippines.

General Gatot - who until now has remained silent - said on Tuesday he had reported what occurred to President Joko Widodo: "Then, well, I didn't have to go."

He said he would now wait for instructions from President Jokowi, as he is popularly known, about when he would travel to the US.

"It's the president who can say I go or I don't. Without (the order of the president) I will not take any initiative."

General Gatot said he was disappointed not to have met with his friend General Dunford. When the pair had last met they had eaten "tasty steak" and US soldiers sung Bengawan Solo, a famous Indonesian song about the Solo River.

"So I wanted to go there to meet with him. But it didn't happen. That's all."

Lowy Institute Research Fellow Aaron Connelly tweeted after the US statement was released that it was becoming increasingly clear that General Gatot - who is believed to have political aspirations after he retires from the military in March - had precipitated an avoidable crisis in order to boost his nationalist credentials.

"If Jokowi (the president's nick name) doesn't back Gatot, he'll appear insufficiently nationalist. If he does, it boosts his political standing."

The incident has fanned outrage in Indonesia with even the English-language Jakarta Post, which is largely targeted at foreigners, describing it as a "diplomatic scandal" in a tart editorial.

"Such carelessness of the US Government may result in fallout in bilateral and defence military ties," the editorial said.

"Close relations between high ranking officials may help control the damage ahead of a possible visit by US President Donald Trump to Indonesia in the near future - but still leave us agog at how the world's biggest power could be so reckless."

Department of Homeland Security press secretary Dave Lapan said efforts were made by US Customs and Border Protection and the US Department of State to address the boarding denial and clear the passenger for travel before the passenger arrived at the airport.

"Unfortunately, he was denied boarding."

Mr Lapan said the issue with General Gatot's boarding approval was "quickly resolved" and he was rebooked on another flight and cleared to board. "He chose not to travel."

"The U.S. Government is dedicated to ensuring that all persons travelling to the United States are screened and properly vetted," Mr Lapan said. "We regret that the passenger and his wife were inconvenienced."

Defence analyst Evan Laksmana said it was still not known what the specific security protocols or problems were, beyond some possible glitch, that had led to General Gatot's initial denial of entry.

"The lack of clarity ??? and the subsequent offence could fester and hound US-Indonesia security relations if left unaddressed," he said,

Natalie Sambhi, a Research Fellow at the Perth USAsia Centre, said the incident boded well for General Gatot domestically because he could capitalise on it as proof of a Western anti-Indonesia conspiracy.

"While Gatot isn't expected to be a strong candidate for the presidential election in 2019, positioning himself to the Indonesian public as the victim of US policies and fanning anti-foreign sentiment will go a long way in bolstering his populist credentials. That could further his chances of joining as a vice presidential candidate."

Follow Jewel Topsfield on Facebook