The defendant, the 65-year-old half-sister of the monarch's daughter, stood accused of "disturbing the peace of the dead" by agreeing to the exhumation in 2012, the Tribune de Genève daily reported.
Mwambutsa, who ruled from 1915 until he was overthrown in 1966, had lived in Switzerland for 12 years when he died and had asked to be buried in the small Alpine nation.
But his daughter and the Burundian government campaigned for the return of his remains to his native country for a national funeral ceremony and had asked the defendant, whose name was not given, to help, the paper reported.
But since 2012, Mwambutsa IV's remains have been stuck in Geneva, since one of his nieces, Esther Kamatari, opposed their transfer to Burundi.
"I believe there are people who were closer to the king, who should determine his fate," the defendant told the court, the ATS news agency reported.
Her lawyer Alain Marti, who is also representing the Burundian government in the affair, called for her acquittal.
"This whole procedure is based on nothing," he said.
"My client only did what her half-sister asked her to do."
The Geneva criminal court will have to decide "between a cherished national reconciliation, of which Mwambutsa IV's remains are the symbol, and these procedures" launched by his niece Kamatari, who is a candidate in Burundi's upcoming presidential elections," Marti added.
The Geneva court should reach a verdict in the case in about two weeks.