Indonesia's military chief was temporarily barred from travelling to the United States at the weekend due to an "administrative error", the U.S. embassy in Jakarta said in an online statement on Wednesday.

General Gatot Nurmantyo was about to board a flight to the United States on Saturday when he was told that the Customs and Border Protection Agency had denied him entry, even though he had a visa and an official invitation from the chairman of the U.S. joint chiefs of staff to attend a conference in Washington.

"General Gatot Nurmantyo and his wife were delayed in their ability to board their flight due to an administrative error. The error was quickly corrected. We have taken appropriate measures to prevent this matter from occurring again," the U.S. embassy said in a statement, without elaborating.

The incident prompted top U.S. officials, including Defense Secretary Jim Mattis and envoys in Jakarta to apologise to Indonesia as it demanded details as to why Nurmantyo was blocked, where he had been able to travel to the United States on official trips before.

U.S. Homeland Security Department said earlier this week that the U.S. embassy in Jakarta had informed Nurmantyo's office that he might be delayed in boarding his flight because of unspecified "U.S. security protocols".

It added that the U.S. government was unable to resolve the problem before Nurmantyo arrived at the airport and he was denied boarding. The general was eventually cleared and booked on another flight but he chose not to travel.

Nurmantyo told reporters on Tuesday that he did not travel on a later flight because he had informed President Joko Widodo of the issue and that he would only travel "on further orders from the president".

"There's no signal (from the president) so I no longer have the initiative to go," Nurmantyo said, adding he was disappointed at not being able to meet his friend and counterpart General Joseph F. Dunford, who had invited him to attend an anti-terrorism conference.