Amer al-Fakhoury, a former member of the South Lebanon Army (SLA), went into exile more than two decades ago before returning to Lebanon in September, when he was arrested.
The 57-year-old was released on Monday over a statute of limitations on his alleged crimes, a judicial source said, though put under a travel ban, according to state media.
On Thursday, US President Donald Trump hailed Fakhoury's return to the United States, saying he was suffering from late-stage cancer.
On Friday, Lebanon's Foreign Minister Nassif Hitti asked US ambassador Dorothy Shea to explain "the circumstances of Amer Fakhoury being transferred abroad from the US embassy," the National News Agency said.
A security source said on Thursday that Fakhoury left the country in a helicopter from the US embassy heading to an unknown destination, but the embassy did not comment on the report.
Read also: South Lebanon Army: Return of war-time 'collaborator' shines spotlight on brutal legacy of Israel's militia
When Fakhoury was arrested, a Lebanese security source said he had served as a senior warden in the notorious Khiyam prison, opened in 1984 by the Christian-dominated SLA after Israel occupied southern Lebanon.
Witnesses accuse Fakhoury of ordering or taking part in beatings of thousands of inmates.
The veteran militiaman's release by a military court on Monday prompted huge criticism on social media.
Powerful Shia movement Hezbollah, largely credited with Israel's withdrawal from southern Lebanon in 2000, said it would be more honourable for the judges involved to resign rather that "succumb to the pressures that led to this decision".
On Friday, the head of the military tribunal resigned over the criticism.
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