The Baron of Perry Parr has stood down from Defra, as well as his post as Deputy Speaker in the House of Lords.
Lord Rooker, a former engineer and lecturer who took up the role in May 2006, was unavailable for comment, but a Defra spokesperson confirmed the move.
New ministers to enter Defra include Jane Kennedy, Huw Irranca-Davies and Lord Hunt of King's Heath in a huge shake-up of the department, which sees it lose much of it environment portfolio to a new energy and climate change department.
National Farmers' Union (NFU) president Peter Kendall welcomed the move. He said: "We are pleased to see government has emphasised the importance of climate change by creating a seat at the Cabinet table. Agriculture and horticulture are at the front-line of climate change and its impacts."
Kennedy, MP for Liverpool Wavertree, is to become minister for food, farming, water and waste, while Irranca-Davies takes up some rural affairs responsibilities.