Movement and land application of manure is a known risk factor for secondary spread of avian influenza (AI) viruses. During an outbreak of highly pathogenic avian influenza (HPAI), movement of untreated (i.e., fresh) manure from premises known to be infected would be prohibited. However, moving manure from apparently healthy (i.e., clinically normal) flocks may become critical, because some egg-layer facilities have limited on-site storage capacity. The objective of this analysis was to evaluate targeted dead-bird active surveillance rRT-PCR (real-time reverse transcriptase polymerase chain reaction) testing protocols that could be used for the managed movement of manure from apparently healthy egg-layer flocks located in a HPAI Control Area. We also evaluated sequestration, which is the removal of manure from any contact with chickens, or with manure from other flocks, for a period of time, while the flock of origin is actively monitored for the presence of HPAI virus. We used stochastic simulation models to predict the chances of moving a load of contaminated manure, and the quantity of HPAI virus in an 8 metric ton (8000 kg) load of manure moved, before HPAI infection would be detected in the flock. We show that the likelihood of moving contaminated manure would decrease as the length of the sequestration period increased from 3 to 10 days (e.g., for a typical contact rate, with a sample pool size of 11 swabs, the likelihood decreased from 48% to <1%). The total quantity of feces from HPAI infectious birds in a manure load moved would also decrease. Results also indicate that active surveillance protocols using 11 swabs per-pool result in a lower likelihood of moving contaminated manure relative to protocols using 5 swabs per pool. Simulation model results from this study are useful to inform further risk evaluation of HPAI spread through pathways associated with the manure movement, and further evaluation of biosecurity measures intended to reduce those risks.