Wie, who shot a 1-over-par 73 in the opening round, had three birdies and six bogeys at the Kochi Kuroshio Country Club course for a 3-over 75. She was tied with 11 others for 68th place with a 36-hole total of 4-over 148.
'Obviously, I'm very disappointed,' Wie said. 'I played as well as I could. I tried my best today, but things just didn't work out.'
Wie was on the verge of making the cut, but things started to go sour on the par-4 17th.
After hitting the fairway with her tee shot, Wie's approach landed in the greenside rough. She chipped onto the green and then missed a 5-foot par putt.
Because of a backlog of players, Wie then had to wait 20 minutes before playing the par-5 18th.
On 18, her drive off the tee went into the right rough. She hit out onto the fairway, but her approach landed in the short rough on the edge of the green and she missed a 6-foot par putt after chipping on.
'I hit the putt the way I wanted to,' Wie said. 'It just didn't break the way I thought it would.'
With a par on 18, Wie could have made the cut.
'I was a bit nervous walking up the 18th fairway,' she said. 'I was just trying to play a good hole and make par, but it didn't work out that way.'
The 16-year-old American is only the second woman to play in a Japanese men's event. Sophie Gustafson missed the cut in the 2003 Casio tournament.
No woman has made a PGA Tour cut since Babe Didrikson Zaharias in 1945. No one even tried again until Annika Sorenstam teed off at the 2003 Colonial, and only Suzy Whaley and Wie have played PGA Tour events since then.
Wie was making her sixth start in a men's professional tournament. She failed to make the cut in three PGA Tour starts, a Nationwide Tour event and a Canadian Tour event. This is her first tournament in Japan.
Despite not making the cut here, Wie said she plans to keep playing in men's events.
'Not making the cut here has not made me want to play in men's events,' Wie said. 'Hopefully, I can learn from the mistakes I made here and come back here.'
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