The flutes, made from bird bone and mammoth ivory, come from a cave in southern Germany which contains early evidence for the occupation of Europe by modern humans – Homo sapiens.
Scientists used carbon dating to show that the flutes were between 42,000 and 43,000 years old.
The findings are described in the Journal of Human Evolution.
A team led by Prof Tom Higham at Oxford University dated animal bones in the same ground layers as the flutes at Geissenkloesterle Cave in Germany’s Swabian Jura.
Prof Nick Conard, the Tuebingen University researcher who identified the previous record-holder for oldest instrument in 2009, was excavator at the site.
He said: “These results are consistent with a hypothesis we made several years ago that the Danube River was a key corridor for the movement of humans and technological innovations into central Europe between 40,000-45,000 years ago.