Securing public funding to conduct research and leading it by being a principal investigator (PI) is seen as significant career development step. Such a role brings professional prestige but also new responsibilities beyond research leadership to research management. If public funding brings financial and infrastructure support, little is understood about the inhibiting factors that publicly funded PIs face given the research autonomy offered by publicly funded research. Our study finds that there are three key PI inhibiting factors (1) political and environmental, (2) institutional and (3) project based. Traditional knowledge, skills and technical know-how of publicly funded PIs are insufficient to deal with the increasing managerial demands and expectations i.e. growing external bureaucracy of public funding agencies. Public funding is no longer the 'freest form of support' as suggested by Chubin and Hackett (Peerless science: peer review and US science policy. Suny Press, New York, 1990) and the inhibiting factors experienced by publicly funded PIs limits their research autonomy. We also argue that PIs have little influence in overcoming these inhibiting factors despite their central role in conducting publicly funded research.