The new rule means that Juba will now charge 9,500 euros for foreigners working in a professional capacity, 1,900 euros for blue collar employees and 950 euros for unskilled workers.
According to the Labour Ministry, the rule came into force on 1 March, but it's unclear as to when the government will seek the money.
According to British newspaper The Guardian, the government is justifying its choice by saying it would bring in more revenue.
"I think it's the part of a story that has been developing for a year and a half regarding the employment of foreigners," says Jok Madut Jok, a political analyst and co-founder of the Sudd Institute. "First, there were a lot of complaints from Sudanese that jobs that are not difficult to perform were given to foreigners. Last year, the Ministry of Labour basically issued an order to expel foreign workers. This was reversed eventually, but I think this rule is the continuation of that policy."
This news comes just days after famine was declared in parts of the country. This is particularly bad timing as nearly half of the population, about 5.5 million people, is expected to lack a reliable source of food by July.
In that sense, local organisations say the role of international NGOs and foreign aid workers is crucial.
"It's a discouraging move and it's negative for humanitarian workers," says Edmund Yakani, the executive director of local charity Community Empowerment for Progress Organisations. "There are 4,000 foreign aid workers in South Sudan and they offer an alternative livelihood for South Sudanese citizens. So in another way, this is denying access to humanitarians. It's really extreme."
South Sudan has a bad track record when it comes to working with aid groups. Last December, the government expelled the country director of the Norwegian Refugee council without disclosing a specific reason.
This led the UN’s humanitarian chief to call for aid organisations to have immediate access to the country.
This could have a negative impact on the work of NGOs in South Sudan. The country is in a dire state, with more than three million displaced due to fighting.
International aid organisations are already opposing the move.
"I think the government sees the international NGOs as totally capable of paying the fee," says Jok Madut Jok. "I think the officials who came up with this idea made a complete miscalculation. [...] I think it will be debated, and if its impact has been demonstrated, the government will be forced to reduce the fee."
Others expect the South Sudanese government to backtrack on the rule. Joel Charny, the director of the Norway Refugee Council USA told The Guardian he was sure "the NGO community is mobilising to have a dialogue with the government to get them to rescind, or not implement, this directive."