The Ministry of Labour issued a new directive on Thursday which will mostly apply to NGO workers in the country, just days after a famine was declared in the country.
The fee hikes are aimed at increasing government revenue, Minister of Information Michael Makuei told AP.
A famine was declared in parts of South Sudan on February 21. Aid agencies said 100,000 people were affected by the famine, which threatens to affect a further one million people in the coming months.
Human Rights Watch previously reported the country's famine was a man-made result of "conflict, warring parties blocking access for aid workers and large-scale human rights violations."
The United Nations has repeatedly accused the government of blocking or restricting aid delivery.
The South Sudanese government reportedly views international aid organisations with suspicion. Minister of cabinet affairs, Martin Lomuro, recently said "most of the (humanitarian) agencies are here to spy on the government."
|A copy of the Labour Ministry directive
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The previous labour minister, Gabriel Duop Lam, resigned from his post and defected to the rebel camp under Riek Machar on February 17. Lam issued a statement at the time, citing "frustrations" with the government's inability to solve the country's problems and restore peace.
South Sudan's foreign minister, Deng Alor Kuol, told UN humanitarian aid chief, Stephen O'Brien on Saturday he would ensure free access to aid organisations to all areas in need.