The victims were carried aboard a specially chartered Malaysian Airlines jet and were to be received in a solemn ceremony. The government has urged people to wear black and observe a minute of silence and prayer to honor the victims.
All 298 people onboard died when the plane was shot down over an area of eastern Ukraine controlled by pro-Russia separatists as it flew to Kuala Lumpur from Amsterdam.
The victims included 43 Malaysians and 195 Dutch nationals.
Malaysia has been spared many of the natural disasters that regularly strike other countries in Asia, but the downing of Flight 17 was the second tragedy to hit the national airline this year following the disappearance of Flight 370 on March 8.
The government was heavily criticized for its response to the missing jet, but won domestic praise for brokering a deal with the pro-Russian separatists to allow for the return of all the bodies on Flight 17 and ensure international access to the black box flight recorders.