Federer, from Switzerland, ousted defending Japan Open champion Wesley Moodie, from South Africa, 6-2, 6-1. Federer is scheduled to play Japanese wild card entrant Takao Suzuki in Friday's quarterfinals.
Suzuki survived five match points before recording a 6-7 (4-7) 7-6 (12-10), 6-1 victory over Germany's Alexander Waske.
In other matches Thursday: Second-seeded Spaniard Tommy Robredo reached the quarters by topping 15th-seeded American Vincent Spadea 6-4, 7-6 (11-9); fifth-seeded Finn Jarkko Nieminen drilled 12th-seeded Argentine Juan Monaco 6-2, 6-3; ninth-seeded Korean Hyung-Taik Lee defeated sixth-seeded Russian Dmitry Tursunov 6-4, 2-6, 6-4; and No. 14 German Benjamin Becker snuck past Czech Jiri Novak 3-6, 6-3, 7-6 (7-4).