Stephen Fitzpatrick, Bali – A plain-clothes Indonesian soldier gave the order to attack an East Timor churchyard where thousands of civilians were sheltering in 1999, resulting in more than two dozen deaths, a survivor of the atrocity claimed yesterday.

Village clerk Emilio Bareto's evidence at a commission into relations between the two countries contradicted that of former Indonesian foreign minister Ali Alatas, who denied there had been any Indonesian military provocation in East Timor's bloody road to independence.

Mr Bareto told the Truth and Friendship Commission's first day of hearings that the soldier urged armed members of the Red and White Iron militia to attack the terrified residents of Liquica, west of the capital Dili, after they refused to give up pro-independence leaders believed to be hiding in their midst.

The refugees had gathered in the churchyard as clashes escalated between groups supporting integration with Indonesia, and those supporting East Timorese independence, in the days leading up to April 6, 1999, when the massacre occurred. The refugees mistakenly believed all sides would respect the neutrality of the church grounds.

Mr Bareto told the hearing in Bali he was not aware of there being any political leaders from the CNRT, or National Council of East Timorese Resistance, among the more than 2000 people who were huddled in the compound and the pastor's house.

The Red and White Iron militia was led by Eurico Gueterres, now in jail for his part in the violence that split East Timor in the period leading up to and immediately after its August 30, 1999, independence referendum.

The commission opened with Mr Alatas, who was adamant that despite comprehensive evidence to the contrary, Jakarta military elements were not involved in the campaign of orchestrated violence that accompanied Indonesia's withdrawal from its former province.

Mr Alatas said the police, not the armed forces, were solely responsible for law and order in East Timor up until and immediately after the 1999 vote, and so it was not possible the latter were involved in atrocities.

Asked after the hearing whether, as foreign minister, he should have known of reports his country's military was involved in arming and supporting pro-integrationist militias, Mr Alatas retorted: "Does your Foreign Minister (Alexander Downer) know everything that is going on around him?"

However, former sub-commander of the Dili-based Aitarak (Thorn) militia, Mateus Carvalho, was adamant in his evidence late yesterday that his pro-integrationist group was armed by the Indonesian military (ABRI, as it was then known).

"For me, as a former ABRI member, it was very easy to get weapons from them," said Mr Carvalho, who also served as village chief in Hera, west of Dili. "Our weapons came from the district military commander."

Mr Alatas said it had been impossible to anticipate the result of the sudden shift in Indonesian policy that led to the 1999 vote. This change came about when former president JB Habibie declared that East Timor should be offered independence by way of a referendum, rather than the "special autonomy" planned in negotiations with Dili's former colonial ruler, Portugal.

Mr Habibie, known for his autocratic decisions, was reacting to a letter from John Howard in late 1998 proposing a partial "trial of independence" for East Timor. Mr Alatas said the Prime Minister's letter was not "in itself" the cause of the switch, but Dr Habibie was angered by Mr Howard's "spirit of overzealousness to send troops".

Indonesia's brutal subduing of East Timor, after the 1975 invasion, was regarded by elements in the Indonesian military for more than 20 years as an excuse for unchecked violence.