The killing comes days after President Salva Kiir threatened to kill reporters "working against the country". Peter Moi is the seventh journalist to be killed this year in South Sudan, where a civil war is ongoing.
A presidential spokesman said the words were taken out of context and police were investigating Mr Moi's death.
Ateny Wek Ateny said a statement would be issued to clarify President Kiir's remarks, made at the airport in Juba before he went to Ethiopia for peace talks to end the civil war.
Mr Moi worked for South Sudan's Corporate Weekly newspaper and was killed at about 20:00 local time (17:00 GMT) on Wednesday night by unidentified gunmen on the outskirts of Juba.
Juba-based journalist Jason Patinkin said on an Africa radio programme that the killing of Mr Moi was a very worrying development for the journalist community in South Sudan, which has seen a steady decline in press freedom since the outbreak of the civil war in December 2013.
The Committee to Protect Journalists (CPJ) says security agents shut down two privately owned newspapers earlier this month as well as a media group that produced a popular radio series.
The media freedom lobby group has also been critical of Mr Kiir's comments, which local journalists believe were connected to media criticism of the protracted peace negotiations.
"The leader of any country threatening to kill journalists is extremely dangerous and utterly unacceptable," the CPJ’s Tom Rhodes said in a statement
