Fingerprint logging started Friday in Shenzhen, the southern Chinese city bordering Hong Kong, and will be gradually implemented elsewhere.
Chinese authorities counted more than 76 million entries and exits last year from foreigners, primarily from South Korea, Japan, the United States and Russia.
The ministry said in a statement that the new requirement was "an important measure to strengthen entry and exit management" that matches requirements in other countries.
U.S. Customs and Border Protection has fingerprinted most foreign visitors since 2004. The agency said on its website that it is conducting tests of facial recognition software and other biometric screening. Japan also began fingerprinting all arriving foreigners in 2007 as a public safety measure.