Indonesia and Australia's leaders this week have signed deals on defence cooperation, and Australia has gifted Indonesia with four refurbished heavy transport aircraft.
While Australia and Indonesia are strengthening their military ties, other nations, such as the Dutch are concerned by the Indonesian military's dismal human rights track record.
Indonesia has had to pull out of a $280 million deal to buy 100 battle tanks from the Netherlands after waiting several months for the Dutch parliament to approve the sale.
Dutch media reports that the majority of parties in the Dutch parliament opposed the deal because of Jakarta's poor human rights record.
Peter King, a research associate in international relations from the University of Sydney spoke to Radio Australia's Connect Asia. He says that the Dutch's concern with human rights in Indonesia harks back to their historical relationship with the region.
"Well the Dutch have been very sensitive to human rights violations in Jakarta. I think there is a historical reason for that." he said.
"They themselves mucked up the whole West Papua issue during their own colonial administration, they held it back from Indonesia and then in the end had to give in to international pressure."
"So they compensate that by kind of indicating that being forced to hand West Papua to Indonesia, even in this post Suharto democratic period has been a risky business because the army continues to dominate affairs so much in West Papua.
The United States and the European Union have similarly imposed military embargoes on Indonesia, says Peter King, for example, those imposed after massacres committed by the Indonesian military in 1991 and 1991.
The US reinstated military sales to Indonesia in 2006, supported by Australia.
"It wasn't a very good idea because the army has continued to abusive, particularly in Aceh for a time, but Aceh got autonomy and a proper peace deal in 2005."
"In West Papua the human rights violations by the military and the police have continued."
Australia has pursued a strategy of working with the Indonesian military with the hope of improving its record on human rights issues that way. But Mr King says the continuing power of the military in Indonesia is a danger to its democracy.
"I think it is long term danger for Indonesian democracy that the military hasn't been brought in to line on these human rights issues, particularly in West Papua now," he said.
"The Government has just been too reluctant to give up its use of military force to get its way in West Papua. It needs to negotiate with the West Papuans rather than use the so-called security approach." Radio Australia