Recent unrest in newly-independent East Timor which claimed five lives is a purely domestic problem and has nothing to do with former ruler Indonesia, Jakarta's foreign minister said.

"It's their internal problems; social-economic problems, high unemployment and the public's too great expectations for economic improvement," Hassan Wirayuda told reporters.

"East Timorese refugees fled to [Indonesian] West Timor and then returned to East Timor. If they create trouble, it's the action of East Timorese citizens," he said.

Wirayuda also said domestic political rivalries might be behind the unrest. "Alkatiri himself has said he believes there isn't any activity [in East Timor] supported or sponsored by Indonesia," the minister said, referring to East Timor Prime Minister Mari Alkatiri.

A gang armed with automatic rifles stormed into the villages of Tiarelelo and Lobano in East Timor's Atsabe district on Saturday night, killing three people including a village chief and his son and injuring several others.

It was the worst violence since the Indonesian military and their local militia proxies withdrew from East Timor in 1999.

Presidential chief of staff Agio Pereira has said the attackers were pro-Jakarta militiamen and those killed were former resistance leaders during Indonesian rule.

Foreign Minister Jose Ramos-Horta has said that former pro-Jakarta militiamen were involved in riots which hit the capital Dili on December 4, although he did not suggest they were acting on Jakarta's orders.

Two people were killed and 25 injured in those riots which began as a student protest against police.

East Timor became independent on May 20 after 24 years of Indonesian occupation and 31 months of United Nations stewardship.