Agents from the National Security Services on Monday ordered the Citizen newspaper to stop printing because of recent articles urging President Salva Kiir to sign a peace deal with rebels, said newspaper editor Nhial Bol.
The Arabic language Al Rai was closed down on Saturday after the government accused one of its employees of travelling to Kenya to join the rebels, said editor Wazir Michael.
Free-Voice, a group that is known for producing a radio drama aimed at promoting peace, also said its premises were also shut down yesterday.
Tom Rhodes of the Committee to Protect Journalists said the space for critical journalism has been shrinking in South Sudan since the outbreak of an armed rebellion.
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"The crackdown presents an ongoing trend where security forces work in near total autonomy and in disregard to the law," he said.
Six journalists have been killed this year in South Sudan.
South Sudan, which gained independence from Sudan in 2011, has been at war since December 2013 as government forces battle rebels loyal to a former deputy president.