General Gatot Nurmantyo was due to attend a conference in Washington at the request of General Joseph F. Dunford, chairman of the US Joint Chiefs of Staff, but the military said he was unable to board his Emirates flight in Jakarta yesterday.
Military spokesman Brigjen Wuryanto said the general was refused entry by the US Customs and Border Protection agency.
Nurmantyo has decided not to attend the conference until the situation is explained, Wuryanto said.
"Shortly before the departure the TNI (military) commander and his wife received a notification from the airline that they were not allowed to enter US territory," Wuryanto told a press conference.
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"The (US) ambassador is currently not in Jakarta so we have asked the deputy chief of mission in Jakarta to come into the ministry tomorrow for clarification," foreign affairs spokesperson Arrmanatha Nasir told AFP.
The US embassy said in a statement it had been in touch with the general's staff about the matter throughout the weekend and working to facilitate his travel.
It said US ambassador Joseph Donovan has apologised to Marsudi for any inconvenience.
"We remain committed to our Strategic Partnership with Indonesia as a way to deliver security and prosperity to both our nations and peoples."
The conference of national defence chiefs is on countering violent extremism.
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 has been rebuked by members of 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.
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