The new charges include taking of hostages, willful killings, causing serious injuries to body.
The Directorate of Public Prosecutions (DPP) has slapped 93 new charges against former Lord's Resistance Army (LRA) commander Thomas Kwoyelo, dropping the earlier 12 charges.
The charges include taking of hostages, willful killings, causing serious injuries to body and extensive destruction of properties in Amuru and Gulu districts all in northern Uganda between 1993 -2005.
Thousands of people reportedly lost lives and properties in activities by the Joseph Kony-led LRA rebel outfit.
When the case came up for confirmation of the charges by pre-trial judge Susan Okalany, the defense lawyers led by Caleb Alaka objected to the confirmation of the charges on grounds that the 12 counts that had been read to Kwoyelo were in breach of the Geneva Convention.
"My lord we have instructions from our client to object to the confirmation of the charges read to him because they are defective under Article 47 of the 4th schedule of the Geneva Convention," said Alaka.
He added that the allegations in the earlier charges against their client implied that there was an international conflict in northern Uganda yet in the summary of evidence there was no mention of the high contracting parties in the conflict.
He said that although it is true that Uganda is a high contracting party in the conflict since it ratified the Geneva Convention and the latest protocol, the other party was not mentioned and LRA was not a contracting party as per the Geneva Convention.
"The charges are highly defective and brought under the wrong law because there was no war declared by any other country. We pray that the case be dismissed and accused be set free," he said.
In reply, the prosecution team led by Charles Kamuli told court that they had since abandoned the earlier charges against the accused and instead amended the charge sheet.
"My lord we have 93 new counts against the accused. The new charges are brought under Article 3 of the Geneva Convention and the Penal Code Act. The conflicts would now be national and not international as earlier preferred against him. There are no new facts in the case," said Kamuli.
He conceded that the charges were not supposed to be brought under Article 2 of the Geneva Convention but rather Article 3 of the convention.
However, Judge Okalany said that she had no powers to dismiss the case as a pre-trial judge but she could only refer the matter to the Chief Magistrates Court or else prosecution tenders in court the amended charges for confirmation.
Kwoyelo was earlier facing charges of war crimes and crimes against humanity before the International Crimes Division (ICD) of the High Court. He has been in detention since 2008 when he was captured.
So far three pre-trial hearings into the case have been held. The first was held in April 2016; second one in August and the third one in September 2016, in Gulu High Court, making this the fourth hearing.
Standing in the dock, Kwoyelo, dressed in a white T-shirt and black pair of trousers, quietly followed the proceedings.
Born in Acut-Omer village in Amuru district, Kwoyelo was abducted in 1987, at the age of 15, and spent over half of his life in the LRA, the last one-and-a-half years under detention by LRA leader Joseph Kony.