"Among the 46 victims, 26 were of Dutch nationality," the ministry said in a statement.
"The relatives of victims have been informed," it said, adding that the nationalities of non-Dutch fatalities would remain private "at the request of these countries' embassies".
The Malaysia Airlines Boeing 777 exploded over insurgent-held east Ukraine on July 17, killing all 298 on board, with the West accusing Russia-backed separatists of shooting it down and Moscow blaming Kiev.
Millions of Malaysians observed a day of mourning on Friday as 43 of their countrymen killed in the disaster were finally brought home.
The identities of some passengers may never be known as the search for human remains has been repeatedly disrupted by fierce clashes between pro-Russian rebels and Ukrainian troops around the crash site.