The history of Indonesian voyages to northern Australia, from the early seventeenth century to the early twentieth century, has been the subject of detailed archaeological research. The major work on the Macassan trepang industry is Macknight (1976). More recent archaeological research on Macassan visits to the Northern Territory was undertaken by Mitchell (1994) and on Macassan activity in Western Australia by Morwood and Hobbs (1997).

The main bodies of literature on the diverse groups of fishermen from Indonesia who have fished in the northwest Australian waters from the early twentieth century until the late 1960s are reports from various newspapers and government archives, an unpublished compilation of material by Bottrill (1993), and publications by Bach (1955) and Bain (1982). Both Bach and Bain devote some attention to foreign fishing and poaching activities in their studies of the northwest Australian pearling industry. Other sources on Indonesian fishing activity include: the records of a 1949 Commonwealth Scientific and Industrial Research Organisation fisheries survey in the Timor Sea (CSIRO 1949), including one publication by the senior scientist in the survey team (Serventy 1952); an account by Lind (1994) who was a resident in the Kimberley region in Western Australia; the Australian Customs Service file on the apprehension of an Indonesian perahu in 1957; and sections of the doctoral thesis by Crawford (1969) which was subsequently published in 2001.

There is also a range of material stemming from research on Indonesian fishing vessels held in museum collections around Australia (see Stacey 1997). The Australian National Maritime Museum in Sydney has the Madurese perahu lete lete Sekar Aman and associated fishing equipment in its collection. Articles and reports from research on the voyage of the Sekar Aman and other Madurese voyages to the Timor Sea region can be found in Mellefont (1988, 1991a, 1991b, 1997) and Scott (1988). The Western Australian Maritime Museum in Fremantle has a perahu lambo,theSama Biasa, which originated in Pepela and was later confiscated and donated to the museum in 1980 along with other collections of fishing equipment. This has vessel has been the subject of research on perahu lambo boat building traditions (Burningham 1989). The Museum and Art Gallery of the Northern Territory (MAGNT) in Darwin has the largest ethnographic collection of Indonesian watercraft and fishing material culture in Australia. Some of the boats in the collection (such as the Karya Sama and the Tujuan) were donated to the museum after being confiscated for illegal fishing activity, and one has been the subject of detailed research (Stacey 1992).

From the early 1970s, the major sources on Indonesian fishing activity in Australian waters are reports and records from various government departments. These include both files and databases on boat apprehensions and prosecutions from the Western Australian Fisheries Department in Broome (cited in literature as the AFS Indonesian Database and the Western Australian Fisheries Files), and the records of the Foreign Fishing Operations Branch of the Australian Fisheries Management Authority held either in Canberra or at the Northern Territory Department of Primary Industries and Fisheries in Darwin (cited in literature as the Northern Territory Fisheries Files). Parks Australia boarding and patrol reports from Ashmore Reef are located at the Commonwealth Department of Environment and Water Resources offices in Canberra. A variety of published and unpublished material is held by the Commonwealth Department of Foreign Affairs and Trade, including a compendium of information compiled in 1988 (DFAT 1988).

MAGNT staff were engaged as consultants to investigate the impact of Indonesian fishing activities on the Ashmore Reef National Nature Reserve for the Australian National Parks and Wildlife Service (Russell and Vail 1988). Their report summarises historical data on traditional Indonesian fishing activities at Ashmore Reef, provides an analysis of the various groups of Indonesians visiting the region during the years 1986–1988, presents data on the status of marine resources targeted by these fisherment, and includes information collected from interviews with 13 perahu crews and captains present at Ashmore Reef during their fieldwork. There is also a separate consultancy report on Indonesian fishing at Cartier Island (McCarthy 1989).

A comprehensive, but as yet unpublished, report by the Fisheries Resources Branch of the Bureau of Rural Sciences, now part of the Department of Agriculture, Fisheries and Forestry, assesses the nature and extent of Indonesian fishing activity in the AFZ based on an analysis of information from various government departments gathered in 1994 (Wallner and McLoughlin 1995a). The report assesses the impact of Indonesian fishing on marine resources in the AFZ and makes recommendations for future management of these resources, ways of improving the information base, and alternative strategies to deal with traditional Indonesian fishermen operating in the MOU area.