This paper investigates the effectiveness of institutionalised financial incentive programmes designed to encourage researchers to engage in high-impact publishing and commercialisation. Five Australian medical research institutes were analysed, three of which were offering financial incentives for high-impact publishing and two offering financial incentives for commercialisation engagement. The perception of incentives for commercialisation and research productivity within the organisations with incentive schemes was compared with that of organisations without these schemes. We found that incentive policies are effective only if researchers already hold desirable goals with regard to their societal contracts, effectively crowding in these behaviours. Researchers also stated that they believed that high-impact publishing and commercialisation engagement were only possible for large groups of authors and fields. For researchers in smaller fields, the current structures of incentives were ineffective as incentives but instead acted as rewards for when these activities did occur. Alternatively, the existence of these incentives offered researchers options for salary remuneration, attracting high-quality researchers and increasing the organisation's level of prestige as a result. It is recommended that institutional incentive programmes should concentrate on controlling field differences in order to effectively influence rather than simply reward researcher behaviour.