There is corruption in the management of the Letters of Credit, Cabinet Affairs Minister Martin Elia Lomoro has said.
The government introduced this in 2012 after the shutdown of oil production.
Under the arrangement, the Qatari National Bank issues credit lines to businessmen to buy essential goods and receives payment from the Central Bank after three months.
Several government institutions, including Nilepet and the Ministry of Finance, manage the Letters of Credit.
Dr Elia says some individuals abused the arrangement.
“Anybody who is corrupt and would bring problem to the people of South Sudan and wants to tarnish the image of the government of South Sudan and has a plan to fail the government; we will cut their heads off,” warned Dr Elia.
The national parliament is still investigating any wrongdoing in the issuing of Letters of Credit.
But Dr Martin says there were traders who received the Letters of Credit but did not deliver any goods.