Two former top Indonesian ministers told a human rights trial yesterday that a savage outbreak of militia violence in East Timor in September 1999 caught the Jakarta government unawares.

Feisal Tanjung and Ali Alatas, respectively the top security minister and foreign minister at the time, said the government did what it could to contain the violence after the announcement that an overwhelming majority of East Timorese had voted for independence.

"The police had already performed their duty well but they were not able to handle [the unrest] because of the immensity of the problem faced," Tanjung said.

"It was a condition of chaos which was very difficult to face ... It was uncontrollable because the number of police and soldiers were insufficient," he said, testifying at the trial of former East Timorese police chief Timbul Silaen.

Silaen is one of 18 officers, officials and civilians either on trial or due to face trial for gross human rights violation in the runup to and aftermath of the August 30 ballot organised by the United Nations.

Silaen is accused of failing to control his subordinates and to halt five massacres of civilians in April and September 1999 in which more than 100 died.

At another trial before the rights court today, prosecutors recommended a 10 year and six month jail for former East Timor governor Jose Osorio Abilio Soares over the same charges. A verdict has still to be passed in his case.

Tanjung said the campaign and the vote itself had gone smoothly. "The number of policemen were enough to handle the usual number of violations but when chaos like this erupted, it was no longer sufficient," he said.

Tanjung, 62, also played down some of his responsibilities at the time. He said his chairmanship of a team – to "safeguard the implementation" of a May 1999 agreement between Indonesia, Portugal and the United Nations on the holding of the vote – was only coordinative in nature.

He said he could not give details of security arrangements in East Timor during and after the polls since that was the responsibility of then-defence minister and military commander General Wiranto. Tanjung and Wiranto are not among those due to face trial.

The local militiamen and some Indonesian military units waged a campaign of intimidation before East Timor's vote to separate from Indonesia and a violent scorched-earth revenge campaign afterwards. At least 1,000 East Timorese are estimated to have died and whole towns were burnt to the ground.

Many witnesses and defendants at the rights trials have portrayed the militia violence as outbreaks of spontaneous fury. Rights groups and others have said senior Jakarta officials organised and directed the militias.

Former foreign minister Ali Alatas told the trial the authorities had expected some "disappointment" after the announcement of the poll result but had not expected such unrest to break out. "There will be winners and losers and the losers, I was certain, would not accept the results," Alatas said.

He said he had warned the concerned ministers and senior officials after the poll that based on initial reports, the pro-Indonesians appeared to be losing and that security should be tightened. "But I think, no one expected the magnitude [of the reaction]," he said.