Three people died after gunmen targeted an aircraft transporting Indonesian paramilitary police at the airport of this remote Papuan regency.
Liberation Army gunmen launched an attack at the Trigana Air twin otter which had arrived carrying 18 Brimob personnel.
Two people, including the pilot, were injured before a gunfire ensued on the airfield between the Liberation Army members and Indonesian security forces.
Three people who died have been identified as migrants from Indonesia's South Sulawesi province.
The Liberation Army said it was responsible for shooting the three people, including a boy, saying he was hit by a stray bullet.
"The shot was targeted at the child's father but the boy panicked and hugged his father and was hit by a stray bullet on his cheek," a Liberation Army report said.
The boy's parents were the other two killed in the violence. They were migrants from South Sulawesi who, according to the Liberation Army, had been established traders in Nduga's township.
A spokesperson for the Liberation Army and the Free West Papua Movment, Sebby Sambom, said their soldiers shot at the man bcause he had pulled out a gun.
"The person from Sulawesi, he took position holding a pistol and tried to shoot the Liberation Army, Free West Papua group... soldiers... That's why the Liberation army shot him Then his wife and son they came and held him. Then his wife was shot..."
The spokesman suggested that the child's death was entirely accidental. However, he alleged that the man killed was one of many migrants from other parts of Indonesia who had come to live in Papua and become undercover intelligence agents assisting Indonesia's security forces in operaions against Papuans.
"We always identify them, we have data," Mr Sembom explained.
"Some Indonesian civillians become businessmen, but they are Indonesian intelligence agents. Indonesian soldiers and police give them small stores or trade house buildings. They're everywhere."
Meanwhile, the attack on the aircraft transporting the paramilitary personnel has been linked by Indonesian officials to the regional elections taking place this week. The paramilitary police had been transported from the Highlands town of Wamena to Nduga to provide security during the elections.
Indonesian officials said that despite the attempt to disrupt the elections, they have been conducted peacefully. However, tensions remain high in Nduga amid bursts of gunfire that have broken out sporadically after the Army dispersed from the airfield following the deadly gunfight.
Nduga is in the Highlands region where the Liberation Army has launched several attacks since last year. Two TNI personnel were killed there last December, prompting reprisal attacks which left two civilians dead and a church burnt.
Around the same time, the Liberation Army declared a general mobilisation of all its soldiers in Papua to carry out operations against the Indonesian state and what it called "the invaders".
As well as independence, the Army's stated goal has been to close the Freeport mine, which is one of the largest sources of revenue for the Indonesian state.