"We deeply regret the inconvenience that this incident caused and we apologize," Erin Elizabeth McKee, Deputy US Ambassador to Indonesia, said Monday.
Gen. Gatot Nurmantyo eventually chose not to fly to the United States despite being rebooked on a new flight after he was denied boarding on the first, according to a Department of Homeland Security spokesperson.
US Gen. Joseph F. Dunford Jr. had invited Nurmantyo to Washington to attend a conference Monday and Tuesday on combating violent extremism.
Nurmantyo and his wife were set to board an Emirates flight in Jakarta for Washington on Saturday evening, reported CNN Indonesia
, a CNN affiliate.
The US Embassy in Jakarta informed Nurmantyo he may "be delayed in his ability to board his flight" because of security protocols, the Homeland Security spokesperson said. US Customs and Border Protection and the State Department were not able to resolve the issue before the original flight departed.
The spokesperson said the boarding issue was quickly resolved "through coordination between the individual's office, CBP, the US Embassy in Jakarta and other US government partners. The passenger was rebooked on another flight and cleared to board. He chose not to travel."
Joseph R. Donovan Jr., US ambassador to Indonesia, apologized to Indonesian Foreign Minister Retno Marsudi "for any inconvenience" to Gatot, the embassy said in a statement.
"We remain committed to our strategic partnership with Indonesia as a way to deliver security and prosperity to both our nations and peoples," the embassy said.
The State Department referred CNN to the statement by the US Embassy and wouldn't comment further, citing privacy concerns.
The Pentagon did not respond to requests for comment.