It was feared that the fee hike would hit aid agencies which are working to deal with the famine
South Sudan will not go ahead with plans to charge foreigners a $10,000 (£8,200) fee for work permits as officially announced in early March.
The plan has been dropped in response to criticism that it would penalise aid agencies, the finance minister said.
The controversial measure was announced just four days after famine was declared in parts of the country.
However, the revised fee will be reviewed by MPs and could be introduced at a later date.
Foreign workers are currently required to pay $100 (£80) for a work permit.
South Sudanese officials argued that the fee was one of the lowest in the region hence suggesting the 100-fold increase.
But the fee hike faced criticism with people saying that it would burden aid workers at a time when the country was most at need.
Finance Minister Stephen Dhieu Dau acknowledged the complaint as part of the reason why the fee increase has been dropped.
"The ministry of finance acknowledges these significant issues... and steps are being taken to formulate the best way forward," Mr Dau said.
Even before the uproar over the fee increase, the officials of the famine-stricken country had been accused of impeding access for humanitarian agencies.
South Sudan is currently facing food shortages and parts of the country are experiencing a famine.
The on-going civil war has compounded the difficulties of dealing with the country's food problem.
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