Indonesia's military chief is free to travel to the United States, the US embassy said Monday, after the general was apparently stopped as he tried to board a flight.

Jakarta has demanded an explanation for the incident after General Gatot Nurmantyo -- who is believed to harbour presidential ambitions -- was refused boarding in Jakarta by the US Customs and Border Protection agency.

Nurmantyo had been invited to Washington by the chairman of the US Joint Chiefs of Staff General Joseph F. Dunford, America's highest-ranking military officer, where he was due to attend a conference.

Erin Elizabeth McKee, acting deputy ambassador to Jakarta, told reporters there were "absolutely no issues" with the general's ability to visit the US.

"General Gatot is able to travel, there are no restrictions, the United States welcomed his participation in the conference that General Dunford invited him to," she said.

Indonesian foreign minister Retno Marsudi said the US ambassador had apologised, but had offered no explanation.

"We have told them that we still demand a clarification and explanation on why the incident happened, we told them we are still waiting," she said.

Nurmantyo will not attend the conference unless this clarification is received, the military said. "If there has been a mistake, there must be an apology, not to the military commander but to the government," a military spokesman said.

Since being appointed armed forces chief by President Joko Widodo in July 2015, Nurmantyo has been at the centre of several controversies. 

Earlier this year he abruptly suspended all military cooperation with Australia in a row over teaching materials, and he has been rebuked by members of President Joko Widodo's cabinet for making misleading public remarks.

Nurmantyo will step down as leader of the armed forces in 2018 and many analysts believe he has political ambitions.