Often beeswax is used to seal small air leaks on some musical instruments. One of the disadvantages of beeswax is that it has a melting point of around 140 degrees Fahrenheit and can therefore flow to other parts of instruments with deleterious effects. Do you know of a nontoxic substitute for beeswax with a higher melting point?
You might try https://en.wikipedia.org/wiki/Polycaprolactone It softens at hot-water temperatures and is safe to handle. (You'll probably need to heat it a bit above that to get to fully liquid.) FDA approved for some applications, so IMHO pretty safe. This material is usually sold in granular form; some names I've seen are Polymorph, ThermoMorph and "friendly plastic."
But especially if this is a wooden instrument, be careful and if possible test on similar materials (to your instrument) before using it on your instrument. My concern is that it'll soak into wood and change the stiffness and thus tone.