Colonel Kumar Lama, 46, who is currently employed as a UN peacekeeper in South Sudan, was arrested at his East Sussex home by the Met Police on January 3. He was due to return to Africa today after a Christmas break.
Lama was today produced in court, charged with two counts of torture, and was remanded in custody.
The Army officer faces trial in Britain under a law that allows prosecution of alleged war criminals.
Col Lama spoke once to confirm his identity at the hearing, according to a report in the BBC.
He was charged with intentionally "inflicting severe pain or suffering" as a public official on two separate individuals.
The offences are thought to have taken place between April and May 2005 and April and October 2005 at Army Barracks in Kapilvastu in Nepal.
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Two diplomats from the Nepalese embassy also attended the hearing where the court heard that the colonel had previously served as a UN peacekeeper in Sierra Leone and twice in Lebanon.
District Judge Quentin Purdy ordered the Army officer to remain in custody before another hearing on January 24.
Yesterday, an angry Nepal summoned the British ambassador and demanded the immediate release of the army colonel.
Deputy Prime Minister and Foreign Minister Narayan Kaji Shrestha said the arrest of Lama in the UK breached the jurisdiction of a sovereign nation as well international norms.
The foreign ministry summoned British ambassador John Tucknott and handed over a 'protest note' over Lama's arrest.
The ministry said the Nepal government has strongly objected to the arrest, which is "sad and shocking".
Nepal's decade-long Maoist insurgency which ended in 2006, witnessed the deaths of almost 15,000 people while thousands more were allegedly tortured or injured.
Some 100,000 people were internally displaced and the fate of approximately 1,400 others remains unknown to this day. Both the army and Maoist rebels were accused of committing atrocities during the conflict. PTI
WAJ