He served as Fisheries Minister from 1997 to 2003, and then as Environment Minister in the Department for Environment, Food and Rural Affairs, but left government in the May 2006 reshuffle. During his time in government, Morley pushed for a series of environmental causes. In 2004, he sought to strengthen the United Kingdom's efforts to purchase legally harvested lumber and aided the launch of a programme to manage flooding and coastal erosion called 'WaveNet'. In 2005 Morley assisted in the establishment of a Governmental Decontamination Service, to provide decontamination and cleansing assistance after chemical, radiological, biological, or nuclear incidents and major accidental releases of harmful materials.