The Attorney General’s Office and the Directorate of Public Prosecutions are contesting the Amnesty Act, which grants pardons to ex-combatants of rebel groups.

The Uganda Amnesty Commission, the body created to dispense transitional justice under the contested law, is against the move and has applied to the Constitutional Court to be enjoined in a suit by the Lord’s Resistance Army commander Thomas Kwoyelo challenging his arraignment in court contrary to the act.

The Amnesty Commission says the move by the AG and the DPP is an underhanded plan to administer justice in a selective manner, a development that could dissuade thousands of rebels from laying down arms.

“What this effectively means is that all those who are benefiting from the amnesty law are doing so illegally and can be arraigned in court and prosecuted any time,” said Nathan Twinomugisha, chief legal officer at the Uganda Amnesty Commission.

In an interview with The EastAfrican last week, Mr Twinomugisha described the move by the AG and DPP to take away the commission’s powers as “going overboard.”

Principal state attorney Patricia Mutesi last month said the amnesty law was created as a temporary instrument and inconsistent with the Constitution and international instruments.

“We have recently learnt that the AG has made a submission in the hearing of Constitutional Reference 36 of 2011 to the effect that the Amnesty Act, Cap 264, contravenes the Constitution of Uganda, insofar as it interferes with the powers of the DPP under Article 120 of the Constitution, and secondly, insofar as that Act purports to prevent the prosecution of certain offences under the Geneva Conventions Act, it is inconsistent with Article 287 of the Constitution,” reads the application, dated August 24.

Amnesty Commission chairman Justice Peter Onega concedes that his outfit was initially set up to last six months, but has since been given several extensions after the government saw the necessity of its existence.

“Was this Commission temporary? Yes, but it was given extensions. The current term expires in May 2012, and if thereafter it went without renewal, there would still be two years to wind up the Commission’s work. That’s what the law says,” said Justice Onega.

Attorney General Peter Nyombi denied any knowledge of the move, but sources have told The EastAfrican that officials in his chambers have been instructed contest the legality of granting amnesty to Kwoyelo, a rebel commander who was captured in combat in March 2009.

This presents a significant departure from the spirit of the Act and the pronouncements of President Yoweri Museveni, who has maintained that all LRA combatants, most of whom were abducted as children and forced into rebellion, are eligible for amnesty.

The only exceptions are the five rebel leaders wanted in The Hague following their indictment for war crimes and crimes against humanity by the International Criminal Court in 2005. The five are Joseph Kony, Vincent Otti (since killed on the orders of Kony), Raska Lukwiya, Okot Odhiambo and Dominic Ongwen. 

The amnesty law, enacted in 2000, grants amnesty to anyone engaged in war against Uganda, and the DPP’s role is to aid this process, provided that the parties have renounced rebellion. Kwoyelo, who was captured in DR Congo’s Garamba National Park, applied for amnesty, which the Commission consented to, but the DPP has refused to sign and absolve the applicant, even after the ICC ruled that amnesty be granted.

Our source indicated that the government is dead set against the idea of granting Kwoyelo amnesty and there have been some behind the scenes manoeuvres to frustrate his application.

“This is hypocritical. This law was brought in good faith to help end the war,” said Caleb Alaka, Kwoyelo’s lawyer.