Nilepet denies the allegations, suggests the evidence collected may have been forged.
South Sudan's government has rejected claims that the leadership has diverted millions of dollars from the national oil company to fund the ongoing civil conflict.
"The report was intended to damage the image of the president and the government of South Sudan," Information Minister Michael Makuei told the BBC.
“We all know that Global Witness is US-funded and America has taken an anti-government stance, and Global Witness is an anti-government organisation," he added.
The report in question linked the state oil company Nile Petroleum (Nilepet), directly to arms transfers and the financial benefit of President Kiir’s closest advisers.
The company, it says, operates in secrecy, and the report details how this secrecy has been used to finance military operations, arms transfers to ethnic militias, and conceal the looting of millions of dollars meant to help imports of essential goods.
South Sudan’s security forces have also been accused of atrocities in the country’s civil war, including ethnic cleansing and rape.
Nilepet has denied the allegations, and suggested the evidence collected may have been forged.