Nearly 400,000 children of school-going age are not in education at present, the agency said, despite an increase of over 50 per cent in enrolment since June.
Currently close to half a million Syrian children in Turkey are attending school.
The agency's deputy executive director Justin Forsyth praised Turkey for this "huge achievement" but said more needed to be done, in a statement on the agency's website.
"Unless more resources are provided, there is still a very real risk of a 'lost generation' of Syrian children, deprived of the skills they will one day need to rebuild their country," Forsyth added.
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Ankara says there are 2.7 million Syrian refugees in the country, of whom 1.2 million are children, according to UNICEF which says it is the country hosting the highest number in the world.
Nearly 180,000 babies were born to Syrian refugees in Turkey between April 2011 and September 2016, the health ministry said, quoted by the state-run Anadolu news agency today.
Earlier this month, President Recep Tayyip Erdogan said skilled Syrian and Iraqi refugees currently working in the black economy would be granted citizenship if they pass security tests.
The conflict in Syria has killed more than 310,000 people since it began with anti-government protests in March 2011.
Across the region, a total of 2.7 million Syrian children are not in school with the majority affected inside the war-ravaged country.
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