Vaudine England, Jakarta – Authorities in East Timor have issued an arrest warrant for Eurico Guterres, the militia leader held by police in Jakarta.

"We're asking the Indonesian authorities to send Guterres over," said Barbara Reis, spokeswoman for the UN Transitional Administration in East Timor (Untaet). "We're waiting for feedback from the Indonesian Government."

East Timor's special panel for serious crime, set up by the UN, wants Guterres arrested over the attack on April 17 last year on the house of independence supporter Mario Carrascalao, which left 12 people dead, and the Liquica massacre on April 6, when militiamen attacked a church and butchered scores of unarmed adults and children.

Commenting on the arrest warrant, a police spokesman said government authorities might refuse to turn Guterres over because of pending legal matters against him in Jakarta. "They could just as well try [to seek the repatriation], but it's not a correct thing to do," Brigadier General Saleh Saaf said.

Pro-Jakarta militias, backed by Indonesian military and police, waged a campaign of terror in the lead-up to East Timor's independence vote, and ravaged the territory after a massive majority voted to end Jakarta's rule.

Guterres is being grilled in Jakarta over the destruction of the UN High Commissioner for Refugees' office in Atambua, West Timor, and the murder of three of the agency's foreign staff last month.

"I'm ready to be tried wherever, even in a court of hell," said a defiant Guterres from his Jakarta cell. "But let me emphasise I am an Indonesian citizen. I don't want to be tried in East Timor and I'm sure the Indonesian Government would not surrender me to East Timor because I have been fighting for the side of Indonesia."

The arrest warrant for Guterres surprised officials in Jakarta. Sources said Indonesia had yet to catch up with the fact that East Timor has its own functioning judiciary, including the special panels for serious crimes. "This is not a United Nations international human rights tribunal, but it is not an ordinary court either," Ms Reis said.

Indonesia insists it will try its own people first – to fend off calls for an international rights tribunal. But Jakarta is also bound by a memorandum of understanding on co-operation signed by Indonesia and East Timor, which says such matters "should be guided by the principle that individuals shall generally be held responsible in the jurisdiction where the crime at issue was committed".

The memorandum commits both states to "undertake to transfer to each other all persons whom the competent authorities of the requesting party are prosecuting for a criminal offence". Jakarta can refuse the transfer request "if the carrying out of legal proceedings by authorities of the requesting party would not be in the interests of justice".

UN sources in Dili said it was a coincidence that their arrest warrant for Guterres was issued after he was detained in Jakarta. Asked why it was not issued earlier, one source said the work simply had not been completed on the relevant cases until now.

Meanwhile, an Indonesian citizen now in a UN jail in Becora, East Timor, is at last receiving medical attention following concern that a gunshot wound to his stomach could kill him in detention. Taryono was remanded in custody on March 31 after wounding two people. Though charged, he has yet to go on trial, and UN officials say East Timor's judicial system is failing to take proper care of its prisoners. Questions have also been raised about the willingness of any hospital in East Timor to accept the prisoner, but sources now say steps are being taken to save Taryono.