The historic artefacts were buried in the 1930s during Mongolia's Communist purge, when hundreds of monasteries were looted and destroyed.
The relics include statues, art work, manuscripts and personal belongings of a famous 19th Century Buddhist master.
The leader of the search team, Michael Eisenriegler, described it as an "adventure of a lifetime".
A total of 64 crates of treasures were buried in the desert by a monk named Tudev, in an attempt to save them from the ransacking of the Mongolian and Soviet armies.
They belonged to Buddhist master Danzan Ravjaa and only Tudev knew where they were hidden. He passed on the secret to his grandson who dug up some of the boxes in the 1990s and opened a museum.
The current Austrian-Mongolian treasure hunt team found two more boxes. Mr Eisenriegler told the BBC World Service they were filled with "the most amazing Buddhist art objects".
"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 latest finds will be put on show at the Danzan Ravjaa Museum in Sainshand, 400km (250 miles) south of the Mongolian capital, Ulan Bator.
About 20 boxes remain hidden in the desert.