The winger left the tournament in Qatar after it emerged that he was under investigation by the Japanese police over an alleged incident in Osaka in 2023.
Ito has denied the allegations and is suing his accusers for 200 million yen (S$1.8 million) in damages.
Japan’s football association said at the Asian Cup that the 30-year-old’s departure was to protect the player and team from a media furore, and that is set to continue until there is a resolution to the issue.
"I made the decision not to call him up to protect him," said coach Hajime Moriyasu.
"When I imagine what the environment will be like surrounding him if he is called up, it will not be an environment where he can play calmly, and not only for him but also for the team. It doesn’t create an environment where the whole team can work together calmly.
"Also, I thought about the impact it would have on his family and the people he values the most, I decided that it would be better not to call him up."
Ito has since been playing regularly for French club Reims but he will now not be able to play for Japan against North Korea in Tokyo on March 21 and in Pyongyang five days later.
The allegations emerged as Japan were preparing to play Bahrain in the last 16 at the Asian Cup. Ito was an unused substitute for the game and left the squad before their 2-1 quarter-final loss to Iran.
He was backed by Reims and has played five times for the French club since returning from the Asian Cup.
Looking ahead, Moriyasu handed a surprise recall to veteran full-back Yuto Nagatomo, who had not been called up since the 2022 World Cup.
The 37-year-old is Japan’s second most-capped player ever with 142 international appearances, behind the retired Yasuhito Endo (152).
Moriyasu retained the services of Zion Suzuki, who made several high-profile mistakes at the Asian Cup and the goalkeeper, whose father is Ghanaian-American and mother Japanese, was racially abused online.
Japan have made a perfect start to World Cup qualifying with wins over Myanmar and Syria.
North Korea lost 1-0 to Syria before thrashing Myanmar 6-1.
The game in Pyongyang will be Japan’s first in the North Korean capital since 2011.