Six others were also put to death.
Febyanti Herewila, who married Chan the day before his execution, was on the flight. She was joined by Sukumaran's parents, brother and sister, who were escorted from the airport by police.
Government officials refused to confirm whether cargo offloaded from the plane did contain the remains of the two men.
Chan and Sukumaran were the ringleaders of a gang known as the Bali Nine, and had been found guilty of attempting to smuggle 8kg of heroin from the island into Australia.
Despite international anger over the executions – and condemnation from the United Nations – Prime Minister Tony Abbott has told reporters he is confident that Australia's relationship with Indonesia can be rebuilt.
"It really was terrible that these cruel and unnecessary executions went ahead. Our anger and our grief, sadly, is not going to bring those two young men back," he added.
Mr Abbott also questioned the "odd" decision by the Australian Catholic University to introduce a scholarship in the pair's memory.
"I know part of Christian faith is forgiveness, but another part of Christian faith is calling people to be their best selves," he said on Friday.
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