The eight-seeded Nishikori will next face Janko Tipsarevic of Serbia, who advanced after Nikolay Davydenko of Russia retired with a left hip injury just four games into their match. The third-seeded Tipsarevic was leading 3-1.
"I don't know what the injury is exactly yet," Davydenko said. "I'm a bit scared as I've never had anything like it before. I will still go to Beijing, maybe wait a few days and see what the pain is like."
Serbia's Viktor Troicki also cruised into the semifinals by beating Dmitry Tursunov of Russia 6-4, 6-4.
The second-seeded Troicki failed to serve out the match at 5-2 in the second set but held on for victory at Putra Stadium.
Troicki will face Marcos Baghdatis of Cyprus, who defeated fourth-seeded Jurgen Melzer of Austria 6-3, 7-6 (3).
Nishikori ousts Almagro in Malaysia Open quarters
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