The 1.2 billion yen (£9.3 million) attraction is the latest development announced by the British company, which has been rapidly rolling out its branded attractions across the world in recent months.
With an area of 4,000 square metres, the centre will open next June inside the Decks Tokyo Beach shopping centre.
Madame Tussauds display
Merlin will temporarily display a selection of waxwork figures at the mall in October. If the display is popular, a Madame Tussauds museum is expected to be brought to the city shortly afterwards.
A company statement said: “If Tokyo residents and international visitors enjoy it as much as the other twelve Madame Tussauds attractions around the world, then Merlin plans to make it a permanent feature.”