They were sterilised as part of a Eugenics Protection Law that was in effect from 1948 to 1996. Some of the victims were physically or cognitively disabled, according to the board that approved their sterilisation. Others had behavioural issues.
Japan on Wednesday passed a law compensating tens of thousands of people sterilised, often without their consent, under a government programme to prevent the birth of "inferior descendants" that remained in effect until 1996.
Many of the victims were physically or cognitively disabled, but others suffered from mental illness, leprosy - now a curable affliction known as Hansen's disease - or simply had behavioural problems.
The law, which states that "we seriously reflect and deeply apologise," promises to pay each victim 3.2 million yen ($29,000) in compensation. It was unanimously passed by Japan's upper house of parliament, after previously passing the more lower house.
Yoshihide Suga, Japan's chief cabinet secretary, told a news conference that Prime Minister Shinzo Abe was set to issue a statement later on Wednesday.
"I would also like to apologise after deep reflection as part of the government that carried out the law," he told a news conference.
Victims have five years to apply
According to the law, victims have five years to apply for the compensation, subject to approval by a board of experts.
Japan's "Eugenics Protection Law" came into effect in 1948 as it struggled with food shortages and rebuilding a ravaged nation, and was only revoked in 1996.
During that time an estimated 25,000 people were sterilised, with at least 16,500 not giving consent, which eugenics board could order if it signed off on the procedures after an often cursory review. Few records remain.
About 20 victims around Japan are currently suing the government for compensation and an apology. The first judgement in one of these cases is expected late in May.
Though the most notorious eugenics laws were imposed by Nazi Germany, Japan is not the only nation with similar programmes in peacetime. But overseas laws were mainly revoked in the 1970s.