On 6 May 2006, Rooker was appointed Minister of State for Sustainable Food, Farming and Animal Health at the Department for Environment, Food and Rural Affairs. He was a controversial choice as minister responsible for animal welfare due to his well-known pro-hunting views. In 2007, following Rooker's appointment, numerous complaints from animal welfare campaigners were sent to the Labour Party. He later also became deputy leader of the House of Lords. He retained both these roles when Gordon Brown became Labour leader and Prime Minister in 2007 but stood down in October 2008.