The announcement was made at a ceremony to mark the launch of a three-day anti-polio campaign in the northwestern city of Peshawar, and is aimed at children from North Waziristan and other Taliban strongholds.
Farakh Sair Khan, a senior administrative official for the restive tribal areas, told the gathering the new strategy would "vaccinate children belonging to areas that are not accessible for the polio workers."
"North Waziristan is affected most by the polio virus and unfortunately we had not been able to vaccinate the children there for security reasons but we are trying to overcome it," Khan said.
As many as 2643 polio teams will be participating in the campaign to vaccinate children under five, he added.
North Waziristan is a stronghold of Pakistan's most feared and ruthless fighters, including the Pakistani Taliban and Haqqani Network, and is virtually inaccessible due to the risk posed by internal clashes and targeted violence against outsiders.
"We will establish over 50 vaccination sites next to the checkpoints of security forces," said Shahdab Younis, an official of the UNICEF told AFP.
"Establishing these sites next to security checkpoints will minimise the risk of attacks," she added.
She said the move would also pressure parents -- many of whom believe polio drops are a Western ploy to sterilise Muslims -- into allowing their children to be vaccinated, due to the intimidating presence of armed troops.
"We have received 37 new cases of polio in the first three months of this year, 33 of them are from North Waziristan," Younis said.
"Polio vaccination was banned in North Waziristan since 2012 and the children there have not been vaccinated against polio since," she added.
Meanwhile, a separate official said talks had begun with the army, whose co-operation would be required.
"We are discussing it with the army because most of the security checkpoints belong to (them)," the official told AFP on condition of anonymity.
Ongoing infighting between two rival militant groups in North Waziristan that started last week left 62 people dead.
According to the World Health Organization, Pakistan recorded 91 cases of polio last year, up from 58 in 2012.
Pakistan's failure to defeat polio stands in stark contrast to its neighbour and great rival India, which recently celebrated the eradication of the disease three years after its last case.
Some 56 people including health workers and police officials providing security have been killed in militant attacks on polio vaccination teams in Pakistan since December 2012.
Militant groups such as the Pakistani Taliban oppose the immunisation drive, saying it is a cover for US spying.