Coffins bearing the remains will arrive on a special flight and be received by the country's king, prime minister and other dignitaries to a minute of silence at Kuala Lumpur's main international airport, Deputy Prime Minister Muhyiddin Yassin said in a statement.
The remains will then be brought to the next-of-kins' hometowns throughout the country where they will be laid to rest, he said.
The 16 victims comprise 15 Malaysians and a Dutch citizen who was born in Malaysia.
More than 220 coffins filled with remains have been taken to the Netherlands for identification, but the search for body parts is still not complete due to fighting around the crash site.
Of those aboard, 193 were Dutch and 43 were Malaysians, including 15 crew members.
Muhyiddin said a further eight Malaysians had already been identified and would be sent back in stages pending completion of forensic work.