Malaysians observed a moment of silence following the arrival in Kuala Lumpur of the bodies of 20 Malaysian victims of Flight MH17 that crashed in Ukraine in July.
A specially chartered plane took off from Amsterdam and landed around 10:00 local time (02:00 GMT).
National flags are flying at half-mast for the day of mourning.
Flight MH17 is believed to have been shot down by a missile fired by pro-Russian rebels. They deny the claim.
All 298 passengers and crew on board the Malaysia Airlines Boeing 777 died on 17 July.
From office workers to train drivers, many among the nation of 30 million observed a minute's silence as white hearses drove the remains from the airport to private funerals in various provinces.
The country's public transportation, including the national rail system and Kuala Lumpur's monorail, paused during the minute of silence.
Prime Minister Najib Razak, who turned his Twitter and Facebook pages black, wrote a condolence message that was widely shared.
"Last month, 43 Malaysian lives were taken over eastern Ukraine. Today we mourn the loss of our people. Today, we begin to bring them home."
"Our thoughts and our prayers are with the families and friends of those who lost their lives. Today we stand with you, united as one."
Transport minister Liow Tiong Lai said in a statement that the government will "redouble" efforts to bring home the remaining victims.
Malaysia Airlines is organising a public prayer session and a spokesman also expressed the company's condolences.
Earlier on Thursday, a contingent of Malaysian soldiers met the plane to escort the coffins to the hearses.
All the coffins were draped in the national flag. Three of the 20 bodies have been cremated in the Netherlands.
The victims' bodies have been given to their families and relatives to be laid to rest.
This is the first time Malaysia is holding a national day of mourning for civilian victims.
The honour has traditionally been accorded only to the royal family and heads of government.
— NBC News (@NBCNews) August 22, 2014
Of the 43 Malaysian victims, 28 have been identified in the Netherlands so far, which is leading an international investigation into the crash in eastern Ukraine.
First bodies of Malaysians aboard MH17 arrive home http://t.co/mdYgMDIZN5
— Huffington Post (@HuffingtonPost) August 22, 2014
More than 200 coffins with remains of the victims have so far been taken to the Netherlands.
But the inquiry is being hampered by continuing fighting between Ukrainian government troops and pro-Russian rebels near the crash site.