When a Japanese citizen marries someone from overseas, the spouse's nationality and name are recorded in the registry system that local governments must maintain by law.
Currently people from Taiwan -- regarded as a region, not a country under a policy in place since 1972 when Tokyo normalised ties with Beijing -- are described as from China.
But "from May, after revisions to ministry rules, a name of a region can be written in the nationality field", a justice ministry official told AFP.
The change follows requests from Taiwanese spouses who want to express their regional identity, he added.
Taiwan's government welcomed the decision, foreign ministry spokesman Hsiao Kuangwei told reporters on Tuesday.
The move will "demonstrate respect for the identity of Taiwanese residents in Japan" and "will also provide greater clarity in identification", he said.
Japan's residence certificates for mid- to long-term foreign residents already allow Taiwanese to describe themselves as being from Taiwan, the Japanese official noted.
"Practical difficulties have also arisen due to discrepancies in the country or region names -- Taiwan on the residence card, and China in the family register," he added.
China regards self-ruled Taiwan as its own territory and has said it will use force to bring the island under its control if necessary.
It opposes any actions that attempt to confer international legitimacy on Taiwan, which Beijing has sought to erase from the global stage.
"We urge the Japanese side to abide by the one-China principle and the spirit of the... political documents between China and Japan," Chinese foreign ministry spokesman Guo Jiakun told reporters on Monday after Japanese media reported the change.
"No gimmicks on the Taiwan question, and do not send any conflicting or wrong signals," he said.
Japan cut official ties with Taiwan in 1972, stating in a joint communique with Beijing that it understands and respects that "Taiwan is an inalienable part of the territory of the People's Republic of China".
However, the country has kept close economic relations with Taiwan, and Taiwanese chip giant TSMC opened a new factory in Japan's Kyushu region last year.
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