The troubled region comprising seven districts along the Afghan border is the epicentre of Pakistan's war against the disease which brought international humiliation earlier this month when the WHO imposed travel restrictions on the country.
After the World Health Organisation restrictions, from June 1, every Pakistan going abroad will have to produce a certificate of having received anti-polio vaccine.
In May, the WHO declared a global "public health emergency" after new polio cases surfaced in Pakistan. The country is responsible for 80 per cent of polio cases diagnosed around the world this year.
"But 369,039 youngsters of North Waziristan, South Waziristan and Mohmand districts will be left out due to deteriorating law and order in these areas," he said on condition of anonymity.
"Some parts of Khyber will also remain inaccessible."
Already at least 66 new polio cases, mostly from tribal areas, have been reported in Pakistan in the year. The country is one of three countries along with Nigeria and Afghanistan where polio virus is endemic.
Taliban violence is the prime hurdle against immunisation of the kids. The militants allege the vaccine is a conspiracy by the West to sterile Muslims.
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