"The government has kicked off its three-day campaign this morning," Al Jazeera's Kamel Hyder reported from Islamabad.
Local Taliban and Pakistani warlord Hafiz Gul Bahadur, whose followers are fighting Western troops in Afghanistan, have banned polio vaccinations in the northwestern tribal region of Waziristan to protest against US drone attacks.
They have condemned the immunisation campaign, which began on Monday, as a cover for espionage.
Difficulties in administering vaccinations saw Pakistan reach its highest rate of polio in a decade in 2011, with 198 new cases, compared to 144 in 2010. Most of the new cases were in the northwest of the country.
The use of the Hepatitis C immunisation campaign as a cover in the hunt for Osama Bin Laden has led the Taliban to view these campaigns as intelligence-gathering exercises, he said.
Shakeel Afridi, a Pakistani surgeon who was recruited by the CIA to help find bin Laden, was sentenced for 33 years on treason charges in May.
"The US drone strikes are continuing in that volatile area," Al Jazeera's Hyder reported. "The Pakistani military has also launched its own campaign, trying to regain those areas from some of the fighters who have held some of those territories."
'Children at risk'
Officials have warned that the Taliban ban could put 240,000 children at risk.
"There is possibility that we may have to skip the polio campaign in North and South Waziristan because we are not getting clearance from the army nor is the situation conducive," a government health official told AFP news agency.
"We have threats from the Taliban. Going to these areas for a polio campaign would be tantamount to putting the lives of our staff in jeopardy," added the official, speaking on condition of anonymity.
Dr. Bruce Aylward, assistant director-general of polio, emergencies and country collaboration at the World Health Organisation, told Al Jazeera that it was important for the government to take heed of the Taliban's concerns over the potential of the campaign being used for intelligence-gathering.
"We need to address any underlying concerns the people may have about the operation. We need to have their people doing the vaccinating, doing the planning, and making sure that they're done in a way that is acceptable to those communities."
"As people come to understand that their children are now the only children in the world at risk of being paralysed for life, and that the local leaders hold the future of those children in their hands, more and more of them will very quickly try and find ways of coming to solutions to get their children vaccinated, but it's going to require getting the leadership involved."
Fawad Khan, director of health services in the tribal belt, told the AFP that at least 160,000 children in North Waziristan and 80,000 in South Waziristan would be affected if polio drops are not administered.
Talks are ongoing between administrators and the Taliban, but health workers had "not yet received the green light" for going ahead in Waziristan, he added.
But a senior security official said tribal elders would on Monday discuss how to launch the campaign.
In South Waziristan, where the army fought local Taliban in 2009, the official said "it should not be difficult" to vaccinate children "at least in areas where displaced persons have returned".
Polio remains endemic only in Afghanistan, Pakistan and Nigeria. The highly infectious disease affects mainly the under-fives and can cause paralysis in a matter of hours. Some cases can be fatal.
The World Health Organization (WHO) has warned that if Pakistani authorities failed to contain the Polio virus, then several countries would be compelled to impose travel and visa restrictions to make sure that the virus does not spread to their countries