Ms Blackman, 22, from Sevenoaks in Kent, was working as a hostess in a Tokyo nightclub when she disappeared.
She called a friend before her disappearance in July saying she was going on a day trip to the seaside with a customer.
Wealthy property developer Joji Obara, allegedly a regular at bars in Tokyo with foreign hostesses, was arrested in October and has been charged with drugging and raping four women since 1996.
Now Tokyo police have found hair that may belong to Ms Blackman in the seaside flat southwest of Tokyo where Obara allegedly raped the four women, said Japanese national newspaper Asahi in a front page report.
Prosecutors have not charged Obara in connection with Ms Blackman's disappearance, but his arrest provoked intense media speculation with the 48-year-old businessman admitting that he had once met the missing woman at a bar.
Citing unidentified sources close to the investigation, the Asahi newspaper said that DNA tests indicated that 20 of 400 strands of blonde hair discovered in the bathroom of Obara's flat were genetically similar to those of Ms Blackman.
Kyodo News agency and the Sankei newspaper ran similar reports.
Emotional appeal
Inspector Toshihiko Mii of Tokyo's Azabu precinct, which is leading the investigation into Ms Blackman's disappearance, declined to comment.
Separately, Obara was indicted for a fourth time on Thursday, charged with raping a Japanese woman in June after giving her drug-laced drinks, prosecutors said.
At his first court appearance on 14 December, he pleaded innocent to raping a Canadian hostess in 1996 and a British hostess in 1997, saying they had consented to sex. He has yet to stand trial for the other two rape charges.
Ms Blackman's father has made a number of emotional appeals for help from the Japanese public during frequent visits to Tokyo.
More than 30,000 leaflets with Ms Blackman's photograph on have been distributed around Tokyo, and her family has put up a £10,000 reward for information leading to her discovery.
The family also set up a hotline in Tokyo and private investigators from both Britain and Japan have helped in the search.