The "Freedom Flotilla" left Australia last month and overnight crossed into Indonesian waters shortly after the Indonesian navy threatened to turn the boat back.
The group said they had completed their mission to present sacred water from the springs of Lake Eyre in central Australia and ashes from Aboriginal tent embassies around the country to West Papuan leaders.
"Evading the Indonesian navy, two tiny boats met near the Australia-Indonesia border to ceremonially reconnect the indigenous peoples of Australia and West Papua," the group said on its website.
"The cultural exchange of indigenous elders was held in secret, due to threats made by Indonesian government ministers and military officials who had stated that the navy and air-force would 'take measures' against the peaceful protest.
Indonesian navy spokesman Untung Suropati told AFP on Thursday that the navy would only use force if threatened by an armed vessel and, if the group were unarmed, they would only be prevented from setting foot on Indonesian soil.
Armed militants have for decades fought an insurgency on behalf of the mostly ethnic Melanesian population in Papua with Indonesian security forces repeatedly facing allegations of torturing political activists.
About 20 activists are involved in the flotilla, including Aboriginal elder "Uncle" Kevin Buzzacott who made the exchange with the West Papua leaders as a symbol of support for the West Papuans' struggle.
The activists hope to dock in the Papuan port town of Merauke and hold a ceremony to raise awareness of what they say are widespread rights abuses at the hands of Indonesian authorities.
However, they have struggled to communicate with Indonesian officials, and protest organiser Izzy Brown said calls to the military via satellite phone and radio had failed.
The boat is still at sea awaiting a response from the Indonesian military on whether it can dock or not.
Jakarta keeps a tight grip on the troubled region, the western part of New Guinea island, where a low-level separatist insurgency has been simmering for decades, and there are high rates of poverty and low standards of health and education.
Papua declared independence from the Dutch in 1961, but neighbouring Indonesia took control of the region with force in 1963. It officially annexed Papua in 1969 with a UN-backed vote, widely seen as a sham.
The "Freedom Flotilla" left Australia's northern city of Cairns on August 17 with three boats but the fleet was reduced to one after two boats suffered mechanical problems.
