"Recent scans confirm an injury to the right knee with bone bruising and possible cartilage damage to the kneecap.
The 32-year-old will return to the UK for further investigations and specialist review," ECB said on its website.
Pietersen will not available for the English side in the third and final Test against New Zealand starting Friday at Auckland.
"The injury is likely to require ongoing assessments and a six-eight week period of rest and rehabilitation. Pietersen has therefore been withdrawn from all cricket including the Indian Premier League," it added.