The measures are similar to the "U.S. Visit" system introduced in the United States after the September 11 attacks in 2001.
In a nod to historical sensitivities, "special" permanent residents of Korean and Chinese origin -- many born in Japan and descended from those brought as forced labour before and during World War Two -- are exempt, as are diplomats and children under 16.
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Fingerprinting of such residents was abolished in 1992 after a lengthy campaign, while fingerprinting of all foreign residents ended in 2000.
"Japanese will get the message that foreigners are incipient criminals," said Choi Sun-ae, a Korean resident of Japan who campaigned to abolish fingerprinting and on Tuesday took part in a protest outside the Justice Ministry in Tokyo.
Unlike the United States, Japan requires resident foreigners as well as visitors to be fingerprinted and photographed every time they re-enter the country, although if they pre-register they can go through a fast-track line.
That has angered many resident foreigners, who have until now been able to line up with Japanese for faster processing.
"My husband is Japanese. I have two Japanese adult children working in Tokyo. I feel slightly insulted," said Briton Jennifer Ukawa, 69, who has lived in Japan off and on since 1969 and also took part in Tuesday's protest.
Britain this month began requiring people applying for UK visas to have their fingerprints scanned and photographs taken digitally.
Some worry that longer lines at points of entry could discourage tourists and business travellers, even as Japan tries to polish its image as a tourist destination and global financial centre.
"Suddenly grouping long-term residents and taxpayers in Japan with occasional visitors risks creating excessive delays for frequent business travellers and imposing unacceptable costs on businesses," said the European Business Council in Japan and the Australian and New Zealand Chamber of Commerce in Japan in a letter to the Justice Ministry.
Immigration officials said the procedures went smoothly on Tuesday morning except for a glitch with one machine and that the average wait was 20 minutes.
