Japan, like many countries, has an interest in excluding agricultural pests. Part of their strategy is to prohibit importing plants and plant material that might harbor the pests. See Regulations when Bringing Plants into Japan from Another Country. Cut flowers, even if not prohibited, seem to require inspection on arrival at Narita.
You can check specific choices of flowers using the database search form at Database for Importing Conditions
You also need to plan for the care of the flowers, including protecting them from physical damage and from drying out. Consideration for your fellow passengers suggests avoiding anything with a strong scent. You will be storing them at 12% humidity for 11 hours. See this answer for some tips.