A flute is an open cylinder air column instrument. This means that an idealised flute, the fundamental pitch of the flute should have a wavelength of twice the length of the flute.
This isn't exactly the case with a real flute though. For example, a standard D4 shakuhachi is around 54.5cm, but the wavelength of D4 is 117.48cm. Double the length is 109cm. This is about 7.8% shorter than ideal (so it should be ~1.5 semi tones high), but the flute still plays in tune. My shakuhachi is 53.3cm and it's still in tune - in fact, if anything it's slightly flat. If you account for the utaguchi the flute is about 5mm shorter again.
I'm not actually sure if Boehm transverse flutes have this difference - I just measured a C flute, and the full length of the sound chamber is about 67cm (slightly longer than the idealised 65.93cm), but the length from the mouth piece to the end is only 60cm, and I'm not entirely sure how the idealised tube length should be defined (I guess it's the length of the cavity, rather than the distance between openings). If it's from the mouthpiece, then the difference is even bigger, almost ~10%.
The shakuhachi has a slightly tapering bore, which a Boehm flue doesn't, so I'm wondering if it's related to that, but I don't understand how it would be. Is there some effect of the narrow bore on the speed of sound? Or is it because the sound actually bounces down the flute at a slight angle, thus lengthening it's path? Are there other parameters that affect the fundamental?