The ongoing conflict between the Pakistan Army and the Taliban has left more than a million children at risk of contracting polio.
As many vaccinations had to be compromised due to the inaccessibility of many violence-affected areas.
The WHO says more than a million children, trapped inside the conflict zone, have been missed.
"Pakistan was the country closest to interrupting the virus. Now we have a challenge, the conflict will create a cluster of children, a cohort, who are susceptible to the virus," BBC quoted Dr Khalif Bile Mohamud, the WHO representative in Pakistan, as saying.
Pakistan is one of four countries, which still see annual outbreaks of polio.
The first few months of the year are crucial for vaccination teams who try to reach children before the poliovirus starts to circulate.
This year, vaccination efforts were badly hit, as Taliban extremists intervened and stopped several polio campaigns, calling them un-Islamic.
Extremists also described the vaccine as dangerous and part of a Western plot to harm Muslim children.
However, the biggest obstacle was the military offensive.
Since the start of the military offensive against the insurgents, many areas, including much of Swat and parts of the tribal areas, have become inaccessible to health teams.
Health teams are trying to vaccinate as many children as possible who have emerged from the conflict zone.
They have already treated about half a million. The aim is to create a firewall of immunity, so, if there are outbreaks they can be contained.
So far this year 20 cases have been confirmed, seven of them from northwest Pakistan.
But this is just the start of the polio season. Most cases are usually reported in late summer and autumn.