The National Institute of Health here said that all three cases were from Khyber tribal district on the Afghan border.
None of the three children had received the polio vaccine as anti-polio workers are not allowed to visit some of the areas which are controlled by Taliban.
The new cases were found at the conclusion of three-day countrywide anti-polio drive which aimed at giving vaccine to 34.1 million children.
But the campaign was cut short to one day in Peshawar and some important tribal areas like Khyber, South Waziristan and North Waziristan were not included in the campaign.
Thousands of others could not be reached due to threats by the militants.
Pakistan recorded 199 polio victims in 2000 and it is feared that the ominous record will be easily exceeded as it is only short of 12 patients.
A total of 58 polio cases were reported in 2012 while 93 cases surfaced in 2013.
Pakistan, which is already facing travel restrictions imposed by the World Health Organisation, is among the three countries along with Nigeria and Afghanistan where polio virus is endemic.
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