Dowsett finished eighth in the time trial at the world championships last month, and narrowly missed out on being a part of Britain's Olympic cycling team.
He says, "This isn't a decision I have taken lightly. Sky is a fantastic team and I was flattered that they wanted me to stay but I have a new opportunity and a new chapter of my career."
His move follows the departures of sporting director Steven De Jongh, and race coach Bobby Julich, who both admitted they had taken performance-enhancing drugs, in fallout from the Lance Armstrong scandal. Senior sports director Sean Yates retired from cycling on Sunday.