Lungu's family had wanted to bury him privately in South Africa, where he died in June. They were left visibly distraught by the Pretoria high court's decision and intend to lodge an appeal.
The Zambian state welcomed the ruling, saying that while it mourned with the former statesman's family, Lungu "belongs to the nation".
The dispute follows a long-standing feud between Lungu and his successor, President Hakainde Hichilema, with Lungu's family saying he had indicated that Hichilema should not attend his funeral.
Handing down the ruling, judge Aubrey Ledwaba said the Zambian government was "entitled to repatriate the body of the late president" and ordered his family to "immediately surrender" it to authorities.
Following Lungu's death from an undisclosed illness at the age of 68, the family wanted to be in charge of the funeral arrangements, including the repatriation of his body, but the Zambian authorities sought to take control.
The government and his family later agreed he would have a state funeral before relations broke down over the precise arrangements, prompting the family to opt for a burial in South Africa.
The former president's elder sister Bertha Lungu cried in court after the verdict was announced.
Speaking over the loud wails, Zambian Attorney General Mulilo D Kabesha said the ruling was not a win for the government but rather "what makes good sense".
"When you are the father of the nation, you can't restrict yourself to your immediate family," he said.
Mr Kabesha praised the court for making a "sound judgment" and said that while the family had a right to appeal, this was a "learning curve" for those aspiring to the highest office.
The family has since said it intends to "appeal against the whole judgment and order" made by Mr Ledwaba.
This means Lungu's body will remain in South Africa until the appeal is heard.
The BBC understands that private security services have been enlisted to protect Lungu's remains at the morgue in Pretoria following repeated attempts to remove the body without authorisation.
Lungu led Zambia from 2015 until 2021 when he lost the election to Hichilema by a large margin.
After that defeat he stepped back from politics but later returned to the fray.
SOURCE/AUTHOR : Khanyisile Ngcobo & Nomsa Maseko - BBC News in Johannesburg
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