Democratic Labour Party Senator John Madigan has urged the Australian Government to not turn a blind eye to Indonesia's treatment of the indigenous population of Papua province.
Foreign Minister Julie Bishop this week signed a Code of Conduct agreement with Indonesia to promote intelligence cooperation and iron out tension over Australian spying activities against Indonesian president Susilo Bambang Yudhoyono and his inner circle.
The agreement is hoped to repair Australia's relationship with Indonesia.
Senator Madigan said the Government should not forget the situation in West Papua, which is facing a conflict similar to the one in East Timor.
"I think we need to learn from past mistakes – the Balibo Five, the annexation of East Timor – the situation that we have in West Papua [is] that we want to see clear, transparent, democratic government," Senator Madigan said.
Two French journalists were jailed this month by Indonesian authorities for not obtaining the correct visa.
Local police had raised concerns the journalists' activities could "destabilise" Papua.
Earlier this month, five separatist rebels were shot dead in clashes with Indonesia's military.
"We've got problems on our own doorstep and yet they don't seem to get a mention," Senator Madigan said.
"I realise, as do the majority of Australians, that we want to develop good relations with Indonesia, but any relationship is based on being able to speak in a robust and truthful manner, otherwise it's a flawed relationship."
The triumph of Indonesia's president-elect Joko Widodo in July's election has raised hopes of improving democracy in the archipelago state, but Senator Madigan said the West Papua situation shows Indonesia still has a way to go.
"Indonesia is on the road to becoming a more vibrant democracy and all Australians would support that, but to become a democracy, you've got to have transparency, and we have ongoing reports that keep coming up regularly of atrocities there," he said.
"We all know the Indonesian nation is a huge, very diverse group of islands and Indonesia, as all governments, has its challenges but we do need to encourage the Indonesian government to act responsibly fairly to all of their people.
"The place I believe we can have the greatest influence in world affairs is initially in our own backyard ... We're talking about people, we're talking about people's lives and I won't be complicit by my silence."
Madigan pushes issue with fellow crossbenchers
Senator Madigan has been raising awareness of the West Papuan conflict with fellow crossbench senators who hold the balance of power in the Senate.
"[Independent senator] Nick Xenophon and I often speak about it – we've had numerous conversations on this issue. I've mentioned it to another of my fellow crossbench senators," he said.
"I think that it's a process of education, it's a process of having calm discussion about this issue, and it needs to happen.
"I have raised the issue of West Papua on numerous occasions in the Parliament in the past three years and I will continue to do so for however long I'm here, until such time as we get some real results for these people."