East Timor's prosecutor general will not investigate claims the country's prime minister was behind deadly unrest that erupted in 2006, saying the allegations are "too political".

Former prime minister Mari Alkatiri has called on current Prime Minister Xanana Gusmao to resign, amid claims he orchestrated the violence that plunged the country into crisis.

Alkatiri quit as prime minister in June 2006 after a request Gusmao, who was then the president, amid claims Alkatiri and some of his ministers gave instructions to arm civilian militia during the crisis.

But last week, rebel leader Alfredo Reinado alleged Gusmao was the "mastermind" who had fomented the 2006 unrest, which left 37 people dead and drove 100,000 from their homes.

Gusmao has refused to respond to Reinado's claims, saying he won't engage in a war of words with the rebel leader.

Prosecutor General Longuinhos Monteiro has told local media his office will not be investigating Reinado's claims about Gusmao's alleged involvement in the unrest because they are "too political".

He said his office would see how the situation with Reinado progresses before initiating any investigation.

East Timor's current President Jose Ramos Horta told ABC radio it was up to the prosecutor general, the ombudsman, and the parliament to investigate the claims. He said he would not ask for Gusmao's resignation.

Ramos Horta met with Reinado last Sunday in Maubisse, 70 kilometres south of the capital Dili. Reinado is refusing to disclose details of the meeting, saying it is up to Ramos Horta to inform the public. Ramos Horta's office have confirmed the meeting took place, but are yet to comment on the details.

Last December, Gusmao announced he would give Reinado "one last chance" to engage in dialogue after the rebel army leader failed to turn up to a meeting.

Security forces have previously failed to apprehend Reinado – a key figure in the 2006 unrest who escaped from jail in August that year – in the hope of starting a dialogue.

Reinado led rebel soldiers after Alkatiri's government sacked more than a third of the country's defence force that year, sparking factional violence.