In 1993, Parkinson became the key person on the Maralinga clean-up project, representing the then federal Labor government (through the Department of Primary Industry and Energy). By 1997, however, there was much cost-cutting involved in the project, and differences of opinion about how the project should proceed, which led to the sacking of Parkinson by the new Howard government.
The clean-up, which involved simply burying untreated long-lived radioactive debris in holes in the ground, was totally unsatisfactory according to Parkinson. He exposed the situation through the Australian Broadcasting Corporation, provoking a strong rebuttal from the government, composed of scientific distortion and personal abuse.