Yes flak was used by pilots and crews in the Japanese theater, specifically Curtis LeMay who said after an incendiary bombing raid, "Large fires observed. Flak moderate. Fighter opposition nil." And if Curtis LeMay was calling it flak it can be assumed pilots under him were doing the same.
Additionally because of the war in Europe, pilots were already equipped with vests called "Flak Vests" even in Japan they were still called that. "Approaching the Japanese coast beneath a quarter moon, B-29 crews tugged on flak vests—heavy, cumbersome garments with steel plates that could stop a shell splinter." link
"LeMay ordered his fliers to go against everything they had been trained to do. There would be no more 32,000-foot daylight raids. The B-29s would become night raiders, and they would come in low. LeMay’s advisors had convinced him that Japan lacked any real low-level flak capabilities, and the enemy fighters would be far less effective attacking the low flying bombers in pitch black darkness at altitudes ranging from 5-9,000 feet." link
Another US pilot Lt. Carter piloting God's Will wrote in his journal that the "flak was intense and rather accurate” and that “about 100 searchlights” were stalking the B-29s.
Carter describing another mission said,"“The fire looked even bigger than the Tokyo fire to me. An area with a diameter of about 30 miles over the target was as bright as day but it had a reddish color. The sky was full of B-29s, Jap fighters, phosphorus flak, shrapnel flak, rockets, tracers and the blackest smoke I have ever seen. It was enough to scare the devil.” link
"It was Major Arthur R. Brashear’s tenth mission. The 499th Bomb Group’s target was the First Fire Zone between the Ara and Sumida rivers. His navigator’s notes summed up most fliers’ reactions to the defenses: “Night incendiary at 5,000 ft. Caught in lights for a short time. All kinds of flak, mostly inaccurate. No hits but this one had us scared!” link