This isn't "allowed" by the contract of carriage, but unless you make a habit of it, you're unlikely to get in trouble with the airline. Since the Czech Republic and the Netherlands are both in the Schengen area, you should not even run into customs/immigration at all and should expect no problems if you do (so long, of course, as you are legally in the Schengen area).

However, any checked luggage will be sent through to Tokyo. Any return portion or further segments of your ticket will be cancelled. If you do this, make sure you do not check any luggage (carry-on only) and understand you will need to make new plans for returning to Prague (assuming you had originally booked a round trip).