They answer (partially) in the faq: https://www.cia.gov/library/publications/resources/the-world-factbook/docs/faqs.html
What is The World Factbook’s source for a specific subject field?
The Factbook staff uses many different sources to publish what we judge are the most reliable and consistent data for any particular category. Space considerations preclude a listing of these various sources.
Why are there discrepancies between The World Factbook's demographic statistics and other sources?
Although estimates and projections start with the same basic data from censuses, surveys, and registration systems, final estimates and projections can differ as a result of factors including data availability, assessment, and methods and protocols. .... and continues.