The 36-year-old Waenga, a 2005 New Zealand Under 21 representative who played 51 first-class matches in 2006-2013, including two in Super Rugby for the Chiefs and 24 NPC matches for Hawke's Bay, as well as more than 30 during three years in France, will control Saturday's Championship final between Taranaki and Otago in Inglewood.
Cottrell will be one of the touch judges, while Hogan will be a touch judge in the Premiership final between Waikato and Tasman.
Pandemic alert levels ruled Auckland and Waikato referees out and resulted in a late change to the appointments, but Hawke's Bay Rugby Referees Association secretary and Hawke's Bay Rugby Union referee manager Keith Groube said those appointed had made it on their own skills and reputations.
"It shows you don't have to come from the main centres," he said.