Michael Eisenriegler, leader of the search team, told the BBC World Service they were filled with “the most amazing Buddhist art objects”.
The expert said: “It is of tremendous value for Mongolian culture because Buddhism was almost extinct in the Communist times, especially in the 1930s.
“I’m totally exhausted right now but I’m also totally impressed with what I’ve seen.”
The finds will be put on show at the Danzan Ravjaa Museum in Sainshand, 400km (450 miles) south of the Mongolian capital, Ulan Bator.
About 20 boxes remain hidden in the desert.