Govinda Prasad Mainali, 46, was tried and cleared of the charges by the Tokyo District Court last month after a DNA test indicated involvement of another man in killing of the woman.
Mainali was freed and sent back to Nepal in June after his request for a retrial was approved and the court cleared him of the charges in his absence.
He filed the request for compensation with the court on Friday under the criminal compensation law that allows a person to seek compensation for wrongful imprisonment at a rate that ranges from 1,000 to 12,500 yen (USD 12-145) per day, Kyodo news agency reported.
The sum is determined after the government considers such factors as the length of time served and degree of mental distress caused.
Mainali is seeking the maximum rate that totals it to around 68 million yen for 15 years. He may also file a lawsuit for damages, according to the report.
The Tokyo District Court initially acquitted Mainali but the High Court, based on the same circumstantial evidence, sentenced him to life in prison in 2000, after he had already spent three years behind bars.
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The country's Supreme Court also finalised the ruling of the High Court.
The victim's corpse was found in a vacant apartment in Shibuya Ward, Tokyo, in March 1997. Mainali, a former restaurant employee, lived nearby and had been acquainted with the woman.
He was arrested by Tokyo police in May 1997 on charges of robbery and murder, and had been seeking a retrial since 2005, the report said.