Abortion is legal in Japan up to 22 weeks but consent is usually required from a spouse or partner, and until now a surgical procedure had been the only option.
The ministry said in a notification to healthcare officials on Friday it had approved the drug made by British pharmaceutical company Linepharma.
The drugmaker filed its product, a two-step treatment of mifepristone and misoprostol, for approval in Japan in December 2021.
Similar medication is available in many countries including France, which first approved the abortion pill in 1988, and the United States, where it has been available since 2000.
The approval of the pill to end pregnancies up to nine weeks follows a ministry panel endorsement, which was postponed for a month as thousands of public opinions were submitted.
National broadcaster NHK said the total cost of the abortion pill and a medical consultation would be around 100,000 yen ($700). Abortions are not covered by public health insurance.
Surgical abortions can cost around 100,000 to 200,000 yen.
The US Supreme Court has temporarily preserved access to the widely used abortion drug, freezing rulings by lower courts that would have banned or severely restricted its availability.
Campaigners in Japan are also pushing for better access to the morning-after pill, which prevents pregnancy.
Emergency contraception cannot currently be bought in Japan without a doctor's approval. It is also the only medicine that must be taken in front of a pharmacist to stop it being sold on the black market.
