Dili – East Timor said on Friday that Indonesian-backed militiamen responsible for hundreds of deaths in 1999 were regrouping and may have been behind this week's violent rioting in the capital.

Foreign Minister Jose Ramos-Horta told Reuters that Wednesday's violence – in which two people were killed and 25 injured – had been carefully orchestrated to discredit the government of the world's newest nation.

"There are growing suspicions that former militias are involved," he said, adding they were made up of elements from Indonesia, which ruled East Timor with an iron fist until the country voted for independence under a UN-brokered referendum in 1999.

"It is not possible that the attack on the prime minister's residence was spontaneous. It was carefully planned a few days before."

A mob of between 600 and 800 torched the residence of Prime Minister Mari Alkatiri as well as another property he rents to a foreign bank and a house belonging to his brother.

Alkatiri said on Thursday he had ordered an inquiry into the rioting and that unidentified "outside influences" were to blame.

The clashes were a blow to efforts to establish a peaceful democracy. The 1999 vote sparked a wave of violence by pro-Jakarta militia groups, backed by the elements of the Indonesian military, in which 1,000 people were killed, according to UN estimates.