Ngor Garang, editor-in-chief of Destiny newspaper, and reporter Dengdit Ayok were arrested in Juba at the beginning of November after Ayok wrote an opinion article accusing the president of "staining his patriotism" by allowing his daughter to marry an Ethiopian man.
National security chief Akol Koor accused the paper of publishing "illicit news" that was defamatory and invaded the privacy of personalities. Garang, who also works for the English-language news website Sudan Tribune, was reportedly beaten while in custody, Amnesty International reported late on Friday.
"Detaining someone simply for criticising the president is an outrageous attack on freedom of expression," said Erwin van der Borght, Amnesty’s director for Africa. The Committee to Protect Journalists (CPJ) said the paper had been closed down despite publishing an apology and suspending Ayok for a month.
South Sudan seceded from the north after decades of civil war on July 9, but rights groups have criticised the southern rebels turned government officials for failing to guarantee the freedoms they fought for.
"It's alarming to see the world's newest nation already arresting journalists under vaguely worded accusations," said CPJ East Africa consultant Tom Rhodes on 8 November.
Kiir denied ordering the arrests and laughed off a question by a local journalist about the case earlier this month.
"(Ayok) might have crossed his boundaries. Defaming the personality of a person, I think, is a crime. And those who arrested him might have acted according to that law," he said.