"It's a really valuable work... long thought to have been lost," said Czech National Museum spokeswoman Sarka Dockalova, adding that staff discovered it in the reserve collection.
"It's a joint composition by Mozart and Salieri, a libretto by Lorenzo Da Ponte put to music," she told AFP, saying it would be performed on Tuesday at a press conference in Prague.
The discovery is especially interesting in light of a legend discounted by historians: Italy's Salieri was said to have fatally poisoned Mozart out of jealousy over the Austrian wunderkind's talent.
First appearing in Alexander Pushkin's 19th-century poetic drama "Mozart and Salieri," the rumour was later featured in the play and 1984 film "Amadeus", which historians say grossly exaggerated Salieri's rivalry with Mozart.
The film was shot in the Czech capital, where Mozart spent considerable time in the 18th century as it was then part of the Austrian Empire.