Nhial Bol, editor of The Citizen newspaper, said security officers closed the paper on Monday.
He said no direct reason was given, but he was later told it was because officials were angry at criticism of the government and the paper's backing of peace efforts.
"They are blaming us for having run a news item which is supporting the proposed agreement," Bol said. "The government is telling us that we should not campaign for the peace agreement to take place."
Radio station Voice of America (VOA), which has offices in the same building, was also affected, journalists said.
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Security officials could not be immediately reached for comment.
South Sudan's civil war began in December 2013 when President Salva Kiir accused his former deputy Riek Machar of plotting a coup, setting off a cycle of retaliatory killings that has split the poverty-stricken, landlocked country along ethnic lines.
Regional mediators, backed by US President Barack Obama during his visit last month to Kenya and Ethiopia, have given South Sudan's rivals until August 17 to stop the bloodshed.
Talks in Ethiopia are due to restart on Thursday, mediators said.
Press rights group AMDISS, the Association of Media Development in South Sudan, condemned the crackdown.
"It infringes the flow of information and undermines the development of the media," AMDISS chairman Alfred Taban said.
International press freedom watchdog Reporters Without Borders ranks South Sudan as the 125th worst nation out of 180.
Rights groups have repeatedly warned that security forces have cracked down on journalists, suffocating debate on how to end a civil war in which tens of thousands of people have been killed.