McKinnon joined the New Zealand Ministry of Foreign Affairs in 1974, and was posted to Beijing as second secretary in 1978. In 1985, he was posted to Washington as First Secretary, then to Canberra as Counsellor in 1986.
McKinnon was Deputy Secretary of Foreign Affairs from 2004, responsible for international politics and security (Programme One). Coupled with his previous role running one of New Zealand's intelligence agencies, he is considered an expert in international security. In October 2006, the Government announced that he would succeed Graham Fortune as the Chief Executive of the Ministry of Defence, a position he held from the end of 2006 to November 2012.[2]