mid-14c., from Medieval Latin flasco "container, bottle," from Late Latin flasconem "bottle," perhaps from a Germanic source (cf. Old English flasce, Old High German flaska, Middle Dutch flasce, German Flasche "bottle"), and if so, perhaps originally meaning "a bottle plaited round, case bottle" (cf. Old High German flechtan "to weave," Old English fleohtan "to braid, plait"), from Proto-Germanic base *fleh- (see flax).
Another theory traces it to a metathesis of Latin vasculum. "The assumption that the word is of Teut. origin is chronologically legitimate, and presents no difficulty exc. the absence of any satisfactory etymology" [OED].