The Monday ruling by Tokyo District Court was the first time a court in Japan has ordered the search giant to alter this aspect of its algorithm, said Hiroyuki Tomita, a lawyer representing the plaintiff.
The court also ordered the US-based company to pay 300,000 yen ($3,100) for the mental anguish experienced by the man, whose identity has been withheld.
The plaintiff claimed that when users begin typing his name, the search engine automatically suggests what they might be looking for.
Clicking through these results takes users to websites that defame the unidentified man, his case said.
Because Google's search functions are not based in Japan, the Japanese court cannot compel it to make the change. Google told local media it was studying the ruling.
Last year, the same court approved a petition by the same man to have his name delinked from autocomplete suggestions, and issued a temporary injunction, which Google did not follow.
This week's ruling is permanent although it can be appealed and is attached to a defamation case that attracts damages.
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