A flute was a musical instrument. It was one of several instruments which the Eighth Doctor could play. (PROSE: The Year of Intelligent Tigers)
Jo Grant incorrectly called the Second Doctor's recorder a flute when it appeared on the Third Doctor's TARDIS console. (TV: The Three Doctors) A confused Sixth Doctor made a similar mistake, while suffering from a time-slip with the Second Doctor. (TV: The Two Doctors)
The Fourth Doctor played out Bach's Badinerie, Orchestral Suite No. 2 in B minor on his reed flute. (TV: The Power of Kroll)
On an Earth-like planet, the Second Doctor played a note on his flute which activated a magnet in the TARDIS. This attracted the belts the fair-haired people of that world were wearing, thus enabling them to pass the second of the tests of Trefus. (COMIC: The Tests of Trefus)