Hollande and Abbott said in a statement they would "respect the sensitivities and values of the two countries and consider the requests" of groups who want the remains returned.
Aboriginal and Torres Strait Islander communities consider the removal of remains to be an insult to their culture and have campaigned for years for them to be returned.
Aboriginal protection group Creative Spirits estimates the remains of some 1,000 peole "were stolen in Australia and illegally exported worldwide until the late 1940s".
The group believes most remains are in collections in Europe and the United States, with the remains of an estimated 53 people somewhere in France.
Meeting during a post-G20 summit tour of Australia, Hollande pledged with Abbott to work within "the specific framework of the France legal system" and to set a committee that would "propose and determine research aimed at identifying the origin of these human remains".
The French government would then "examine possible solutions to enable the return of the human remains in question to their communities of origin".