"The way we are handling these matters is contrary to our customs and a deep disappointment to my grandfather and his ancestors," Mandla Mandela said in a statement, as his 94-year-old grandfather, South Africa's first democratically elected black president, remained in critical condition in a Pretoria hospital.
"It is important at all times that we as a family avoid actions and decisions that will infringe on the dignity of my grandfather," the younger Mandela said.
"Regrettably and reluctantly I am compelled to go to court and respond to the action taken against me," he said.
At the heart of the dispute is Mandela's reported desire to be buried next to his children, the Los Angeles Times reported.
The court order, issued Friday, requires the three bodies to be returned to their original resting place, in a Mandela family cemetery in Qunu, the village in South Africa's Eastern Cape province where the elder Mandela grew up and later retired.
The Nobel Peace laureate says in his autobiography, "Long Walk to Freedom," Qunu is where he spent his childhood's happiest moments.
Mandla Mandela had the bodies, including his father's, exhumed in 2011, allegedly without letting other family members know, and reburied 15 miles away in Mvezo, where Nelson Mandela was born.
Mandla Mandela, who is chief of Mvezo, has been building a Mandela museum in the village to attract tourists.
He has said he promised his grandfather he'd improve the lives of those in Mvezo through development, and the museum is a part of that effort.
South Africa's Sunday Times reported some village elders and local chiefs believed the former president's prolonged ill health could be attributed to ancestors' anger at Mandla Mandela's moving of the bodies.
"Mandela's soul is not at peace. The ancestors will only be appeased once the remains of the Mandela family are reburied in Qunu. Only then will Tata be released," one of the chiefs told the newspaper.
"Tata" means father. Nelson Mandela is often called the father of South Africa.
Nelson Mandela's oldest surviving daughter, Makaziwe, and other family members got the court order Friday to return the bodies to Quru.
But Mandla Mandela, who wasn't in court that day, claims he didn't receive a hearing notice that was left outside his locked front gate.
The three Mandela children whose remains are under dispute are a daughter, also named Makaziwe, who died in infancy in 1948; a son Madiba Thembekile, who was killed in a car accident at age 24 in 1969; and Makgatho, Mandla Mandela's father, who died at 54 of an AIDS-related illness in 2005.
The elder Mandela has three surviving daughters.
Nelson Mandela was admitted to the hospital with a lung infection June 8.
South African President Jacob Zuma said Saturday the gravely ill former leader remained "critical but stable."
"We hope very soon he will be out of the hospital," Zuma said.