'Long live Lobato'
Lobato's three co-defendants, Marcos Piedade, Francisco Salsinha and Francisco Xavier Diegas, face similar charges of involvement in arming civilians during the violence that erupted in Dili in April and May following protests over the then prime minister's dismissal of 600 soldiers.
The four could face a maximum 47-year prison sentence if convicted.
Hundreds of Lobato's supporters from the ruling Fretilin party arrived in dozens of trucks, buses and on motorcycles, waving Fretilin flags and shouting "long live Rogerio Lobato, long live Fretilin" as 50 UN and local police stood guard in and around the court building.
Lobato is one of the founders of Falintil, the armed wing of the then pro-independence Fretilin movement which fought against Indonesian occupation and later turned into a political party.
A report from a UN inquiry into the violence said Mari Alkatiri, the former prime minister, and Lobato were among officials who should be investigated over possible involvement in the distribution of weapons.
Thirty-seven people were left dead in battles between security forces during street violence. More than 150,000 people fled their homes and 3,200 Australian-led peacekeepers were deployed in May to restore calm.
Their numbers have since been reduced to about 1,100.