It is hoped the studies will work how to effectively power areas that have had several failed attempts at establishing reliable electricity supply.
The Indonesian Clean Energy Centre of Excellence was opened in the popular holiday destination of Bali, with a memorandum of understanding signed recently.
The collaboration will trigger a host of research projects to start supporting sustainable energy development in both countries, as the recent release of draft criteria for the Northern Australia Infrastructure Facility showed remote electrification in the tropics is also important to Australia.
The two Indonesian sites will be studied under the leadership and coordination of Professor Pujo Semedi, Dean of Arts at Gadjah Mada University in Yogyakarta, energy markets researcher Dr Ariel Liebman and anthropologist Dr Max Richter, both from Monash University.
One site is in an isolated area of West Kalimantan in Borneo where Pujo and his students have been working for many years.
The second is a group of villages on the island of Kai Besar between Darwin and West Papua.
The centre is also investigating the neighbouring island of Kai Kecil in another project focusing on food security. To get to these islands involves a flight from Ambon to Kai Kecil and another three or four hours by boat.
"It's not that there's no electricity, it's more complicated than that," Richter, who is also Monash Asia Institute deputy director, said.
"For example, there have been several attempts to establish reliable electricity supply on Kai Besar. There's a grid, poles and wires and even a photovoltaic solar array, but somehow it has failed repeatedly. So supply cannot be guaranteed."
He said there were also socio-cultural and economic considerations, such as if a village acquired a mechanical maize grinder, which automatically throws up a host of questions such as how might this change the nature of social interaction? Or who owns the grinder? Who do you charge for the electricity use? Who is responsible if it fails?"
As the problem of remote electrification is multi-pronged, so is its investigation. At the local level, the researchers have been talking to the people and particularly the village heads to ascertain their attitudes and needs.
However, providing resources also demands planning and management at the national level.
Richter said he had become interested in the regional level, where local and national meet and interact.
In the case of the Kai Islands, this is the province of Maluku whose capital is Ambon, a city he has connected with and studied over many years.