"In the disaster-stricken area on the Nepalese side, the number of Chinese citizens missing is nearly 100," ministry spokesman Lin Jian told reporters.
The Chinese embassy was "seeking further verification" from Nepali authorities, he added.
On the Chinese side, authorities said earlier Thursday that 558 people including 260 foreigners were missing after a wall of mud and debris swept over buildings in the trade hub of Gyirong near the Tibet-Nepal border.
Lin said there were "tourists and pilgrims" among the missing foreigners, adding that specific details were still being verified as search-and-rescue operations were ongoing.