East Timor's new defence minister has called for an inquiry into what he called "very serious allegations" involving Prime Minister Mari Alkatiri.
The allegations come amid ongoing unrest in East Timor
Australian media reported on Thursday that an armed group of men was claiming to have been recruited to eliminate Mr Alkatiri's political opponents.
Defence Minister Jose Ramos Horta said he doubted the allegations, but an independent inquiry was needed.
Mr Alkatiri denies the charges, saying people are trying to "demonise" him.
The allegations come amid continuing unrest in East Timor, sparked my Mr Alkatiri's decision to sack 600 soldiers in March.
Their protests led to gang and ethnic violence, mainly in the capital, Dili, in which at least 20 people have died. Thousands have fled their homes to seek safety.
'Hard to believe'
The allegations were first made on Thursday, when 30 armed men told an Australian Broadcasting Corporation reporter that former interior minister Rogerio Lobato had recruited them to help eliminate political opponents of Mr Alkatiri, including the 600 sacked soldiers.
Mr Lobato stepped down on 1 June after President Xanana Gusmao assumed responsibility for the army and police in a bid to end the violence.
Feb: More than 400 troops strike over pay and conditions
March: Government sacks nearly 600 of 1,400-man army
April: Rioting by sacked troops leaves five people dead
May: Violence intensifies, with battles between gangs from east and west of the country
24 May: Government asks foreign troops to take control
Mr Ramos Horta, who is also Foreign Minister, said the president should now initiate a full investigation.
"I find it very hard to believe that our prime minister would arm civilians, individuals and in particular give orders to assassinate others no matter who they are," Mr Ramos Horta told Australian television.
He suggested that the inquiry could be carried out with international assistance, possibly from the United Nations.
Australian Foreign Minister Alexander Downer played down suggestions of Australian involvement in any investigation.