They did not say the game is disrespectful. They were worried that if players can deface of destroy a temple or harm people with a katana ingame, they might be inspired to do it in real life too. Ubisoft released a patch that now made shrines indestructible.

The response from the prime minister is really just about being worried people copy the ingame behavior of destroying a shrine, to real life.

So saying “Japan” says the “game is disrespectful” is just not true.

Source: https://www.gamesradar.com/games/action-rpg/assassins-creed-shadows-draws-attention-of-japans-prime-minister-who-says-defacing-a-shrine-is-out-of-the-question-in-real-life-but-politicians-acknowledge-freedom-of-expression-must-be-respected-in-the-game/