Indonesia has demanded that the United States explain why the Indonesian armed forces chief, General Gatot Nurmantyo, was blocked from travelling to Washington last Saturday, said Foreign Minister Retno Marsudi.
"For us, there were two different issues. The first was to resolve that the ban no longer exists, but the second is that we are still asking for a clarification, an explanation, on why the incident happened," said Ms Retno.
The minister was speaking to reporters yesterday after meeting US Deputy Ambassador to Indonesia Erin Elizabeth McKee, who was summoned to the Foreign Ministry in Jakarta earlier in the morning.
Ms McKee, representing US Ambassador Joseph Donovan, who was away, expressed regret for the treatment of Gen Gatot, who was told he could not travel to the US despite having been invited to Washington by General Joseph Dunford, the US Joint Chiefs of Staff chairman.
"We deeply regret the inconvenience that this incident caused, and we apologise," she said.
"We have resolved the matter, General Gatot is able to travel, there are no restrictions and the United States welcomes his participation in the conference that General Dunford had invited him to." She also added that the US Embassy is "working very hard to understand what transpired in this incident, and we hope that it will not happen again".
Ms Retno said the US Ambassador had apologised for the incident in a phone call on Sunday, and reiterated the importance of Indonesia's relationship with the US.
The US Embassy in Jakarta also posted a statement on its website on Sunday apologising for the inconvenience caused. Indonesia had sent a diplomatic note to the US Secretary of State at the weekend and summoned the US Ambassador to explain the incident.
Gen Gatot, who is due to retire in March, is a popular but sometimes controversial public figure in Indonesia.
Last month, he made it compulsory for troops to watch an anti-communist propaganda film made during the Suharto era, a move critics said could revive a "Red Scare" in Indonesia. He has also held a longstanding belief that Indonesia faces "proxy wars", where foreign states seek to undermine his country by manipulating non-state actors.
The apologies from the US did not seem to placate supporters of the general, whom many had touted to have political ambitions.
By yesterday afternoon, banners protesting against the US over the incident were spotted in downtown Jakarta, including one that said: "Expel the US Ambassador." But they were later taken down by city officials.
Ms Retno said Jakarta is now waiting for the US to investigate and explain why Indonesia's military commander was denied entry.