Iran-based Behrouz Mehri won two prizes in the photojournalism feature category for his images of street children and heroin addicts in the strife-torn southern Pakistani city of Karachi.
Myanmar-based photographer Soe Than Win was awarded a merit in the same category for a series of pictures of democracy leader and Nobel laureate Aung San Suu Kyi.
The 16th annual awards were organised by the city's Foreign Correspondents' Club, the Hong Kong Journalists Association and Amnesty International Hong Kong.
The competition, which was open to Hong Kong and Macau-based journalists as well as foreign correspondents working in Asia, drew 226 entries published or aired during 2011.
More than 1,000 journalists and news organizations from around the world have competed in the Human Rights Press Awards since their inception.
The latest success by AFP follows on from the Pulitzer prize awarded to the Afghan photographer Massoud Hossaini. Massoud Hossaini had already won an award, along with two other AFP photographers Yasuyoshi Chiba and Pedro Pardo, from the World Press Photo 2012 contest.