RadioLive general manager Jana Rangooni said she was extremely pleased to have Mr Joiner joining the breakfast team.
"Cliff Joiner is a news heavyweight who brings a wealth of journalistic experience to our breakfast programme and RadioLive, which I'm very excited about."
Mr Joiner has been at TVNZ since 2007, when he shifted from TV3.
Mr Flannery's job of overseeing One News, Close Up and Q+A is expected to be handed to an Australian news executive this week.
His departure has amplified the usual Christmas shake-up because he has taken with him former Breakfast host Paul Henry and Close Up producer Sarah Bristow.
Last week, TVNZ political editor Guyon Espiner quit to work as a reporter on TV3's 60 Minutes. His replacement has not yet been found.
No decision has been made on a role for New York correspondent Tim Wilson when he arrives home. He is being replaced by Jack Tame.