The disaster killed 15,900 people, with 2,520 people still listed as missing as of the end of February, according to the National Police Agency.
Teeth and fragments of jaw were discovered in February 2023 in the northern region of Miyagi, a spokesman for the local police told AFP.
"After dental and DNA identification analyses, it was confirmed the remains belong to Natsuse Yamane, female, who was six years old at the time," he said.
The girl had been at her home in Yamada, a town around 100 kilometres (60 miles) away in Iwate Prefecture, when the tsunami swept her away, the spokesman added.
She had been listed as missing ever since.
The remains were found by construction workers sifting through material amassed in a clean-up of coastal areas, the Asahi Shimbun daily reported.
The child's family issued a statement of thanks.
"We are very happy to have been contacted and to receive this news after having given up hope," the Asahi Shimbun quoted the statement as saying.
The last time remains were identified in the three prefectures hardest hit by the disaster -- Iwate, Miyagi, and Fukushima -- was in August 2023, the Asahi said.
The 9.0-magnitude earthquake in March 2011 also sent three reactors into meltdown at the Fukushima nuclear plant in this century's biggest atomic disaster.
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