One of the victims is an year-old baby from Peshawar, capital of Khyber-Pakhtunkhwa province.
"She has not been administered the oral polio vaccine (OPV) because of her mother's unwillingness," said a local health workers who refused to be named due to security reasons.
The second victim is from Khyber tribal region which borders Peshawar. She was also deprived of OPV because of her family's reluctance.
The people in traditional northwestern region avoid anti polio vaccine due to fear of Taliban who consider polio medicine as a conspiracy by the West to sterile Muslims.
Pakistan has already been facing travelling restrictions due to threat of polio virus exportation.
The government has announced emergency measures to tackle the disease but so far it has failed to turn the tide, as evident by the record number of new cases.
Peshawar remains the hub of polio virus and the insurgency by Taliban have badly impacted the efforts to vaccinate the children.
Polio is an endemic in Pakistan, Afghanistan and Nigeria.
