Court of Appeal judges, in a two-to-one ruling, have ordered Monitor Publications to pay $120,000 in damages to Pius Bigirimana over a string of articles published from 2012 to 2015, believed to be the biggest such financial ruling against the media in Uganda.
The stories related to a corruption scandal which saw $40 million stolen from a project to rehabilitate northern Uganda after a bloody insurgency waged by the Lord's Resistance Army (LRA) of former child soldier Joseph Kony against President Yoweri Museveni.
Lead judge Elizabeth Musoke said Thursday that the Monitor had portrayed Bigirimana, a permanent secretary in the prime minister's office at the time the embezzlement became public, as "a corrupt, deceitful and untouchable civil servant".
Bigirimana has never been charged and veteran leader Museveni has described him as a whistleblower in the case rather than a suspect.
"I find that the (Monitor), in publishing the 15 defamatory stories about (Bigirimana) for a prolonged period of three years, acted in disregard of his rights and their actions warranted punishment," Musoke said.
Monitor Publications is a private media house which has often had run-ins with the government and has in the past been branded an "enemy publication" by Museveni.
"In stripping away the protection of qualified privilege and fair comment, the ruling undermines the ability of journalists to report about things people in power are doing," Monitor Publications head of editorial policy, Daniel Kalinaki said in statement Sunday.
"We believe the Supreme Court judges will do the right thing for the country, its constitution, and its citizens."
Kalinaki said the ruling was a further a threat to media in Uganda, where censorship, arrests of journalists and their harassment by security forces are common.