Pietersen was included in the 50-over party for the five-match series in India next month following his successful ‘reintegration’ into the national set-up, but will not head to New Zealand as selectors look to manage the workload of key players.
The 32-year-old also missed the recently-concluded Twenty20 series in India.
Pietersen faces a hectic schedule over the next year-and- a-half, with England due to play 15 Tests, including home and away Ashes series, a one-day tour of the West Indies, on top of the India and New Zealand series, and compete in a home Champions Trophy before they attempt to win the World Twenty20 in Bangladesh.
Added to that is the Indian Premier League, which starts in April.
With Pietersen absent, James Anderson, Jonathan Trott and Graeme Swann have returned to the 14-man one-day squad after being rested for the India series.
National selector Geoff Miller said: “Following on from the ODI tour to India, the tour to New Zealand will require players to adapt to different conditions and will prove a real challenge for the squad as we look to continue the progress we have made in limited overs cricket recently.
“There are a number of players who we have decided not to select for parts of the competitive programme this winter as we look to manage their workloads effectively while ensuring we remain competitive.
“We feel this is the best way of keeping players as physically and mentally fresh as possible during a demanding 2013 and beyond.
“This approach also provides an opportunity for talented young players to gain more international experience which will be important for their development and the development of England sides in the future.”
England’s three-match ODI series begins on February 17 in Hamilton.
The 14-man T20 squad features two changes from the party selected for the recent series against India with Stuart Broad returning from a heel injury to captain the side and paceman Steven Finn also back in the fold.
Yorkshire’s emerging batsman Joe Root has received further recognition by being put in charge of England Lions.
The England and Wales Cricket Board announced a 15-man England Lions squad for the limited overs tour of Australia in February which will be captained by Root, who made his Test debut earlier this month against India and also featured in Saturday’s thrilling T20 win against India.
Essex teenager Reece Topley is in the party, alongside Gary Ballance, of Yorkshire, Varun Chopra, Ben Foakes, Toby Roland-Jones and Chris Wright.
New Zealand tour – England T20 squad: Broad (Notts, capt), Bairstow (Yorkshire), Bresnan (Yorkshire), Briggs (Hampshire), Buttler (Somerset), Dernbach (Surrey), Finn (Middlesex), Hales (Notts), Lumb (Notts), Stuart Meaker (Surrey), Morgan (Middlesex), Patel (Notts), Tredwell (Kent), Wright (Sussex).
England ODI squad: Cook (Essex, capt), Anderson (Lancashire), Bairstow (Yorkshire), Bell (Warwicks), Bresnan (Yorkshire), Stuart Broad (Notts), Jos Buttler (Somerset), Finn (Middlesex), Kieswetter (Somerset), Morgan (Middlesex), Patel (Notts), Swann (Notts), Tredwell (Kent), Trott (Warwicks).
England Lions squad: Root (Yorkshire, capt), Ballance (Yorkshire), Borthwick (Durham), Briggs (Hampshire), Chopra (Warwicks), Coles (Kent), Foakes (Essex), Hales (Notts, Harris (Middlesex), Kerrigan (Lancashire), Toby Roland-Jones (Middlesex), Ben Stokes (Durham), James Taylor (Notts), Topley (Essex), Wright (Warwicks).
England’s last-ball win: Page 9.