Vaccinating too few children in Syria against polio because the six-year-old war there makes it difficult to reach them risks causing more cases in the future, the World Health Organization (WHO) said on Friday, posing a dilemma after a recent outbreak.

Two children have been paralyzed in the last few months in Islamic State-held Deir al-Zor in the first polio cases in Syria since 2014 and in the same eastern province bordering Iraq where a different strain caused 36 cases in 2013-2014.

Vaccinating even 50 percent of the estimated 90,000 children aged under 5 in the Mayadin area of Deir al-Zor would probably not be enough to stop the outbreak and might actually sow the seeds for the next outbreak, WHO's Oliver Rosenbauer said.

Immunisation rates need to be closer to 80 percent to have maximum effect and protect a population, he told a briefing.

"Are we concerned that we're in fact going to be seeding further future polio vaccine-derived outbreaks? ... Absolutely, that is a concern. And that is why this vaccine must be used judiciously and to try to ensure the highest level of coverage," Rosenbauer said.

"This is kind of what has become known as the OPV, the oral polio vaccine paradox," he said.

The new cases are a vaccine-derived poliovirus type 2, a rare type which can emerge in under-immunised communities after mutating from strains contained in the oral polio vaccine.

"Such vaccine-derived strains tend to be less dangerous than wild polio virus strains, they tend to cause less cases, they tend not to travel so easily geographically. That's all kind of the silver lining and should play in our favor operationally," he said.

All polio strains can paralyze within hours.

Syria is one of the last remaining pockets of the virus worldwide. The virus remains endemic in Afghanistan and Pakistan.