Duck populations are considered to be a reservoir of Highly pathogenic avian influenza (HPAI) virus H5N1 in some agricultural production systems, as they are able to shed the virus for several days without clinical signs. Countries endemically affected with HPAI in Asia are characterised by production systems where ducks are fed on post-harvest spilled rice. During this scavenging process it is common for ducks to come into contact with other duck flocks or wild birds, thereby providing opportunities for virus spread. Effective risk management for HPAI has been significantly compromised by a limited understanding of management of moving duck flocks in these countries, despite of a small number of recent investigations. Here, for the first time, we described the management of moving duck flocks and the structure of the moving duck flock network in quantitative terms so that factors influencing the risk of HPAIV transmission can be identified. By following moving duck flock farmers over a period of 6 months in Java, Indonesia, we were able to describe the movement of flocks and to characterise the network of various types of actors associated with the production system. We used these data to estimate the basic reproductive number for HPAI virus spread. Our results suggest that focussing HPAI prevention measures on duck flocks alone will not be sufficient. Instead, the role of transporters of moving duck flocks, hatcheries and rice paddy owners, in the spread of the HPAI virus needs to be recognised.