Mark Dodd, Dili – Pro-Indonesian paramilitary groups formed and in some cases armed by the Indonesian military are continuing their campaign of violence and intimidation only days away from the signing of a United Nations-brokered agreement for a ballot on self-determination for East Timor.

Medical staff at the Catholic Motael clinic in Dili were forced to move two patients into a safe house on Saturday night, fearing an attack on the small unguarded surgery following telephone threats by paramilitaries.

The two patients, who are independence activists, were the victims of a militia rampage through the streets of the capital on April 17 which left up to 30 people dead.

There were also unconfirmed reports that two people had been killed and several houses burnt on Saturday at Hera, 12 kilometres west of Dili, the scene of previous violence by pro-Indonesia groups.

Portuguese and Indonesian diplomats will sign an agreement on Wednesday paving the way for the deployment of a small UN monitoring force to supervise the August 8 ballot on self-determination for East Timor. Australia is one of several countries which will contribute at least 50 civilian police to help supervise polling procedures and report on security.

Spiralling violence in East Timor by pro-Indonesian paramilitary groups has claimed more than 100 lives since January's promise by Indonesia's President B.J. Habibie offering the 800,000 people who live there a say in their future.

Human rights workers warned yesterday that Aitarak (Thorn) militia had gathered outside the home of Mr Aniceto Guterres, chairman of Dili's Foundation for Legal and Human Rights. About 30 Aitarak militiamen have set up a guard post next to the Guterres home, in a poor area of town close to the municipal market. Several gang members had been drinking heavily and the arrival of four journalists was not welcomed.

The driver of this correspondent's car had his life threatened and his door kicked, and a Reuters television cameraman and news photographer were ordered to leave.

A Melbourne Age photographer, Jason South, and this correspondent were also ordered to get back in the car and to leave after a militia member fired a warning shot from a homemade pistol. Other gang members displayed knives and clubs hidden under their jackets. No police were in the area.

Human rights officials later telephoned to say Mr Guterres had evaded the militiamen to attend Sunday mass but remained concerned for the safety of his family after nightfall. He has been the target of militia threats following reports linking the Aitarak and other paramilitary groups to a series of bloody attacks on supporters of pro-independence groups in recent months.

A senior police officer said six people had been arrested in the coffee-growing town of Gleno, in the Ermera highlands, on Saturday over the abduction and murder of 11 men, the victims allegedly supporters of pro-Indonesian militias.

The police commander of the Ermera district, Lieutenant-Colonel Erry Gultom, said the six suspects were local youths and members of the pro-independence umbrella group the National Council for Timorese Resistance and an armed wing, Falintil. "During interrogation these people said that the victims were from Besi Merah Putih [Red and White Iron] or Mahidi [Life or Death Integration] – at least in principle they were pro-integration," Lieutenant Gultom said.

"During this incident [allegedly on February 28] the victims were bound and beaten and then taken to the place where they were killed. So far we have arrested six people. We are still investigating their status and position – in this case whether they are actually the killers or accomplices."

But the pro-independence guerilla commander Ular has denied Falintil responsibility for the deaths. Ular admitted his men had captured the 11 men in December following a student-led free speech forum, but said they had been released in February, when they were killed by pro-integration militias and the Indonesian military. "It is not our responsibility, we did not kill them," Ular said.

Dili-based human rights groups said they had been told of the arrests and would investigate the killings – a rare case in which the victims are said to be autonomy supporters.