Police confirmed that Diing Chan Awuol, who wrote online opinion pieces for newspapers and blogs, was shot in the face on Wednesday morning.
It was the first time a journalist has been killed in South Sudan since it gained independence from the north in July last year.
Journalists have frequently complained of harassment and detention by the new nation’s security services. Last year, the authorities closed a newspaper after it criticized President Salva Kiir for allowing his daughter to marry a foreigner.
In his last piece, published by the Paris-based Sudan Tribune website, Awuol broached a sensitive subject by calling on Kiir’s government to foster better ties with its old foe Sudan and refrain from supporting rebel groups there.
The Khartoum government says the south backs rebels in two Sudan border states. The south denies this and South Sudanese newspapers usually support that stance.
A week before his death, Awuol, who wrote under the pen-name Isaiah Abraham, complained that unknown men were attempting to silence him, his brother William Chan said.
“He said he had received threats by phone. (They said) ‘either stop writing or we will get rid of you’,” Chan told Reuters.
Police spokesman James Monday said an investigation had begun and police were yet to identify the shooter or establish a motive. No property was stolen from Awuol’s house, Monday added.
The New York-based Committee to Protect Journalists (CPJ) called on the government to investigate.
“By getting to the bottom of this murder and bringing the perpetrators to justice, authorities in South Sudan can demonstrate their commitment to the rule of law and freedom of expression,” said the CJP’s East Africa consultant, Tom Rhodes.
France-based Reporters Without Borders ranks South Sudan 111th out of 179th in its 2011-2012 press freedom index.
Rhodes said he feared press freedom was declining as the country’s economic situation worsens and a government still unaccustomed to criticism was becoming more intolerant of it.
In January, South Sudan shut down oil production, the lifeline of the young republic, after tensions escalated with the north over pipeline fees.
The two countries later came close to war.
Negotiators from Sudan and South Sudan are meeting in Khartoum this week to try to end a deadlock over how to improve border security, a step both say is needed to resume oil exports from the landlocked south via the north.