American Morikawa, playing his first tournament since the Ryder Cup, started his round at Narashino Country Club with a double bogey before dropping another shot on the fourth hole.
But he fought back with eight birdies to just one more bogey to card a 66, putting him on 7-under overall and within striking distance of sole leader Justin Suh.
Morikawa said that his comeback "shows that my head's in the right space".
"I'm very happy with how everything kind of came about, and obviously the nice little string of birdies was a nice momentum swing," he said.
"The par putt on 17, the putt on 18, all these things are just great little momentum things heading into tomorrow."
Morikawa, who led after the first round of the 78-man, no-cut event on the outskirts of Tokyo, found himself in trouble straight away.
First, he played a shot that nestled against a tree, then three-putted when he managed to get onto the green.
He said "that stuff shouldn't happen but it did", but was encouraged by his response.
"I knew I was still hitting my irons good, I just had to give myself opportunities," he said.
"Just seeing good shots, seeing quality shots go forward, that's important."
Suh carded a 67 to move to 9-under, one shot ahead of Eric Cole and Beau Hossler.
Xander Schauffele plummeted down the leaderboard after a 75 that left him 1-over overall.
The Tokyo Olympics champion, who is also playing his first competition since the Ryder Cup, had a bogey on the second hole before hitting a double bogey two holes later.
Schauffele had another three bogeys to one birdie before the end of his round.
Defending champion Keegan Bradley also faded out of the picture after a 73 that left him even par overall.
Hideki Matsuyama, the 2021 champion, was even further back on 3-over.
Things went better for Suh, who had five birdies to two bogeys and said he was "satisfied" with his performance.
"I think overall throughout the day we just tried to find fairways, greens," said the American.
"Obviously in the beginning I missed a few greens but I was on the correct side and I thought making those critical up-and-downs were huge in the beginning."
