The remains were taken from Ainu grave sites primarily in Japan's northern island of Hokkaido, but also from the Sakhalin and Kurile Islands (now part of Russia) between 1873 and 2011 for anthropological research, especially on the skulls.
At the centre of the controversy is Hokkaido University, which is holding the majority of the remains - those of 1027 individuals - and a lawsuit has been filed against the university by a group of Ainu from the Kineusu kotan seeking to have the bones returned.
The Ainu are the indigenous people of Japan's northern island of Hokkaido and also the Kurile and Sakhalin Islands of Russia's far east.
They are a distinct ethnic group to the Yamato Japanese and have lighter skin, more body hair and rounder eyes, giving them a more European appearance, although recent DNA research suggests they are not actually Caucasian, but of "proto-mongoloid" genetic stock.
The Ainu were an ancient hunter/gatherer society with their own language, culture and a religion based on natural phenomenon - although it is believed there are now almost no native Ainu speakers left alive.
Until the 18th century, the Ainu lived in relative isolation on Hokkaido and maintained a society independent of the Japanese although extensive interactions through trade, and some conflict, did occur.
Then after the Meiji Restoration in 1868, Hokkaido was formally annexed by the Japanese and in 1899 the Hokkaido Former Aborigines Protection Act was passed.
This law marked the beginning of the end of traditional Ainu culture and society, and led to forced assimilation of the Ainu into mainstream Japanese life and the loss of customary hunting and fishing rights.
It wasn't until 2008 that the Japanese diet finally passed a resolution formally recognising the Ainu as the indigenous people of Japan.
The current Ainu population of Japan is estimated to be somewhere between 25,000 and 200,000.
|Dec 13||Japan kanji of the year is 'ring' after Olympics bid|
|The annual "kanji" Chinese character of the year in Japan went to "ring" on Thursday, after Tokyo's successful bid to host the 2020 Olympics, often referred to in local print media as "five rings." (Straits Times )|
|Dec 13||Shibuya revelers face New Year's curbs|
|Tokyo police say they will restrict public access around the main intersection outside Shibuya Station between 10 p.m. Dec. 31 and 2 a.m. Jan. 1 to prevent a crush of New Year's revelers forming for the countdown, a recurrent problem in recent years. (Japan Times )|
|Dec 13||New Tokyo-Ueno rail link may confuse passengers|
|The opening of an additional railway link between JR Ueno and JR Tokyo stations in spring 2015 will drastically change services of the Tokaido, Tohoku and other lines and may cause confusion among passengers. (Yomiuri )|
|Dec 12||Japan hangs two convicted killers|
|Two death-row inmates were hanged Thursday in the fourth round of executions since the launch last December of Prime Minister Shinzo Abe's government, Justice Minister Sadakazu Tanigaki said. (Japan Times )|
|Dec 12||Japan man's $185,000 burglary haul to feed 120 cats a gourmet diet|
|A Japanese man went on a year-long burglary spree, making off with a haul worth $185,000 to feed 120 cats a gourmet diet, police said Thursday. (The National )|
|Dec 13||Man arrested for cutting schoolgirl's skirt in train car|
|Police in Chiba Prefecture said Thursday they have arrested a 41-year-old man for cutting the skirt of a junior high schoolgirl on a train. (Japan Today )|
|Dec 12||Milwaukee rape ruling bolsters victims in Japan|
|A 12-year battle for justice took an enormous financial, emotional and physical toll, says Catherine Jane Fisher. But for the Australian teacher of English and mother of three, it's time to savor a landmark court victory. (womensenews.org )|
|Dec 12||Shoplifting accounts for 10 percent of all criminal offenses in Japan|
|The number of shoplifting cases accounted for nearly 10 pct of all criminal offenses recognized by Japanese police, with the rate increasing, a National Police Agency survey showed Wednesday. (Jiji Press )|
|Dec 12||Hate speech campaigns causing conflicts in Japan: police|
|Hate speech campaigns have intensified in Japan, causing increased conflict with opponents, the National Police Agency said Wednesday. (Jiji Press )|
|Dec 12||Chiba policeman arrested for stalking ex-girlfriend|
|A Chiba prefectural policeman has been arrested for repeatedly sending emails to his former girlfriend following their breakup. (Japan Today )|
|Dec 11||Tokyo man arrested after picking up teen prostitute at Ikebukuro 'JK rifure' parlor|
|Tokyo Metropolitan Police on Wednesday announced the arrest of a Tokyo man for picking up a teen prostitute he met a specialty massage parlor in Toshima Ward. (Tokyo Reporter )|
|Dec 11||Yokohama man nabbed for filming up co-ed's skirt, uploaded 1,000 photos to Net|
|Tokyo Metropolitan Police on Monday announced the arrest of a 36-year-old man for recording photos inside the skirt of a female college student in Setagaya Ward. (Tokyo Reporter )|
|Dec 11||Miss International 2013 kicks off in Japan|
|The Miss International 2013 beauty pageant has begun in Tokyo, Japan, on 7 December. Over 72 contestants will compete with each other for the 53rd Miss International title. (ibtimes.co.in )|
|Dec 11||Japan school cancels student exchange with U.S. city over memorial|
|A high school in western Japan has canceled a student exchange program with its U.S. sister city following a disagreement over a memorial dedicated to World War II "comfort women." (Kyodo )|
|Dec 11||Japan battles rising tide of Chinese illegal immigrants|
|Japanese authorities are fighting against an increasing number of illegal immigrants from China, which is in turn fuelling the drug trade. (Journeyman Pictures )|