The government of Indonesia and the Japan International Cooperation Agency launched a three-year project (2008–2011) to strengthen the surveillance of human avian influenza cases through a comprehensive surveillance system of local-priority communicable diseases in South Sulawesi Province. Based on findings from preliminary and baseline surveys, the project developed a technical protocol for surveillance and response activities in local settings, consistent with national guidelines. District surveillance officers (DSOs) and rapid-response-team members underwent training to improve surveillance and response skills. A network-based early warning and response system for weekly reports and a short message service (SMS) gateway for outbreak reports, both encompassing more than 20 probable outbreak diseases, were introduced to support existing paper-based systems. Two further strategies were implemented to optimize project outputs: a simulation exercise and a DSO-centered model. As a result, the timeliness of weekly reports improved from 33% in 2009 to 82% in 2011. In 2011, 65 outbreaks were reported using the SMS, with 64 subsequent paper-based reports. All suspected human avian influenza outbreaks up to September 2011 were reported in the stipulated format. A crosscutting approach using human avian influenza as the core disease for coordinating surveillance activities improved the overall surveillance system for communicable diseases.