Jose Ramos-Horta, who is also the defense minister, met for two hours with Vincente "Railos" da Concecao, who claimed his men had been recruited and armed by Prime Minister Mari Alkatiri last month to wipe out political opponents.
Alkatiri has vehemently denied the allegations, saying they were part of a broader plot to blacken his name and overthrow the government, the AP reports.
East Timor has been hit by unrest and political tensions since March, when Alkatiri fired 600 soldiers - nearly half the entire armed forces - after they staged a monthlong strike to protest alleged discrimination in the military.
The dismissed troops clashed with security forces in the streets of the capital, Dili, and the violence quickly spread to the general public, with machete-wielding gangs torching houses and looting government buildings and warehouses.
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