The 37-year-old former middle-order batsman had filled the role on a temporary basis recently and the stint had earned him a full-time contract, the board said in a statement.
On Wednesday, the NZC extended Mike Hesson's contract as New Zealand's head coach by two years, putting him in the role until April 2017.
"The West Indies and NZA tours were his first as a coach at that level, and we're very happy with his development," NZC head of cricket Lindsay Crocker said.
"He's been awarded his two-year contract on that basis and I'm confident he'll continue to form an excellent coaching trio with Mike (Hesson) and Shane (bowling coach Shane Bond)."
McMillan played 55 tests and 197 one-day internationals between 1997 and 2007.
(Writing by Sudipto Ganguly in Mumbai; editing by Ed Osmond)
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