He held a Certificate in Banking Administration (ABIA) from the ANZ Staff College in Sydney, a Bachelor of Arts in Public Administration and Sociology from the University of the South Pacific in Suva, Fiji, and a Master of Arts in Defence and Security Analysis from Lancaster University in the United Kingdom.
His first senior appointment, from November 1984 to April 1986, was as Commanding Officer in the Fiji Battalion with UNIFIL peacekeeping troops in Lebanon.
In November that year he was appointed Colonel Adjutant and Quarter-Master General in the Fiji Headquarters, and held this position till January 1991.
The second, in 1991, was as Adviser to the Ministry of Home Affairs, concerning the review of Fiji's cooperative defence relationship with other Pacific countries.
From July 1992 to April 1994, he was posted as Counsellor to the Fiji Permanent Representative to the United Nations Mission in New York City.
In 1994, the Department of Peacekeeping appointed him as Military Adviser to the United Nations Secretary General's Peace Envoy to Afghanistan.
In January 2004, Waqanisau was appointed Chief Executive Officer of the Ministry of Home Affairs, Immigration, and Disaster Management.