Matsuyama, who trailed by a stroke after the first round following a 64 on the par-70, 7,041-yard Narashino Country Club course, had a two-round total of 8-under 132.
Temperatures dropped to as low as 12 degrees Celsius (53 Fahrenheit) late in the second round.
Cameron Tringale birdied his final hole for a 66 and was in second place. Matt Wallace birdied his final three holes for a 69 and tied for third with Brendale Steele (68), two behind Matsuyama.
Joaquin Niemann shot 71 after an opening 64 and was tied for fifth, three strokes behind.
“It was tough, I couldn’t feel my hands and it was really cold,” said Niemann, who bogeyed his first two holes.
Matsuyama made his shot of the day Friday from heavy rough on the eighth hole — his 17th — putting his low shot about 20 feet from the pin before watching his birdie putt drift just right, On his final hole, he left another birdie putt short.
Two days ago at his pre-event media conference, Matsuyama foreshadowed a strong performance despite some recent mediocre finishes.
“If my game scored 10 out of 10 at the Masters, now I would say it scores less than 1,” he said. “I will be struggling this week, but I am here in Japan, so I am motivated to be in contention.”
Hiroshi Iwata, who led by one stroke after the first round, just missed an eagle putt on the 18th and finished with a birdie for a 73 and was four behind Matsuyama.
British Open champion Collin Morikawa shot 68 and was seven strokes behind.
Tokyo Olympic gold medal winner Xander Schauffele, playing in the same group at Matsuyama, shot 74 and was 12 strokes behind the Japanese star.
Only three of the top 20 in the world are playing in Chiba, the PGA Tour’s only stop on the Asia swing.