The impact of the next influenza pandemic may be mitigated by inducing immunity in individuals prior to the start of national epidemics using a pre-pandemic vaccine targeted against current avian influenza strains. The US Department of Health and Human Services (HHS) intends that pre-pandemic vaccines will be allocated to states in proportion to the size of their population in predefined priority groups, i.e. approximately pro-rata. We show that such an equitable policy is likely to be the least efficient in terms of the number of infections averted. We demonstrate that the potential benefits could be substantial if a fully discretionary policy is allowed, i.e. if some regions are allocated sufficient vaccines to achieve herd immunity while other regions are allocated no vaccine. Since such an inequitable policy may be impractical, we consider the sensitivity of an intermediate policy (in which 50% of the stockpile is allocated on a pro-rata basis) to key transmission uncertainties. The benefits of the 50% discretionary policy are sensitive to parameter values which cannot be known in advance. Therefore, despite substantial potential benefits of non-pro-rata policies, our results suggest that the current HHS policy of pro-rata allocation by state is a good compromise in terms of simplicity, robustness, equity and efficiency.