Carlos Belo, the former bishop of East Timor's capital, Dili, has testified that pro-Indonesian militia and Indonesian soldiers, in uniform or civilian dress, were part of much of the unrest. Former East Timor bishop accuses Indonesian soldiers
"The establishment of these groups began to create an atmosphere of intimidation and violence across the entire territory," he said, referring to the militias.
Belo, who won the Nobel Peace Prize for his work on East Timor, said that militias and soldiers attacked a church filled with refugees, killing at least five in April 1999 in Liquica, west of Dili.
"Militia and members of the Liquica military command attacked the church," he said through a translator.
Belo said militias and soldiers rampaged when the results of the independence referendum were announced in September 1999, and that Dili's dioceses was torched the following day.
Some 1,400 people were killed during the 1999 United Nations administered vote for independence, after a majority of Timorese chose self-determination following 24 years of occupation by neighbouring Indonesia.
The Indonesian-East Timor Truth and Friendship Commission, which held its first hearing last month, aims to establish the truth about the violence.
The commission, in Jakarta, is due to hear from Indonesia's president at the time, B J Habibie, on Tuesday.