The 18-year-old young Indian paddler overcame stiff resistance from higher-ranked Hamamoto before prevailing over 9-11 11-9 11-7 10-12 11-3 12-10 in the quarterfinals.
Manika, who won a bronze at the Commonwealth Championships here earlier in the month, will take on another Japanese Ayane Morita in the last-four stage.
In the pre-quarters, Manika had defeated Germany's Theresa Kraft 13-11 11-3 11-9 10-12 11-7.