The 21-year-old was set to feature in the fifth T20I but the youngster had to hospitalised late Tuesday night after he complained of chest pain, breathing difficulties and coughing.
Naseem played just the first match of the seven-match series against England in Karachi and was then rested for the next three matches.
"Naseem has been diagnosed as having pneumonia and the medical panel is now monitoring him. They will decide about his future participation in matches and accompanying the team to New Zealand," the PCB said.
Pakistan is already without their premier fast bowler Shaheen Shah Afridi, who has been out of action since mid-July due to a knee injury and is presently rehabilitating in the UK.
Both Shaheen and Naseem have been named in Pakistan's World Cup, while Naseem is due to go with the team to New Zealand as well.
Medical experts say recovery from pneumonia varies as a patient can be back to doing his normal work in a week or two or it could take him four to six weeks to make a complete recovery as the disease affects the lungs.
Patients who recover from pneumonia are known to complain of tiredness and exhaustion for even two to three months after making a recovery.