The England medical staff will meet on Friday to discuss the 32-year-old's injury, which has already ruled him out of the final Test against the Black Caps in Auckland and the Indian Premier League season.
It is not thought at this stage that he will require surgery, but he is still having to wear a brace to aid his recovery.
With the two-Test series starting at Lord’s on May 16, the decision has been made to give Pietersen time to recover before the Champions Trophy in June as he continues his rehabilitation from significant bone bruising to his right knee.
The England batsman will have a repeat scan next week to determine when he is able to resume training.
An ECB statement said: "England and Surrey batsman Kevin Pietersen has been ruled out of the upcoming Investec Test series against New Zealand as he continues his recovery from significant bone bruising to his right knee. Pietersen will have a repeat scan next week to determine when he is able to resume training."
Pietersen, who is currently in Dubai, tweeted: "Injuries are a sportsman's worst nightmare! This one is hurting me the most.."
In response to supportive messages he received on the social networking site, Pietersen wrote he was "trying" to be fit for the Ashes series and that he had his "fingers crossed".
England’s first match in the Champions Trophy is against Australia at Edgbaston on June 8 which Pietersen is likely to target for his international return, with a hectic summer of Test cricket also including the home Ashes series, which gets under way at Trent Bridge on July 10.
Spinner Graeme Swann's elbow injury will be assessed as England's centrally contracted players have their annual fitness reviews at Loughborough next week after his surgery in America, but he is also unlikely to recover in time to play against the Black Caps.
There was, however, a boost for Andy Flower’s men as Tim Bresnan came through his first serious bowling spell of the summer on his comeback from a winter elbow operation in a friendly against Lancashire at Headingley.