Sentry said the report followed a two-year undercover investigation to look into the financing of African conflicts.
South Sudan's government said it was deeply concerned by the release of a report by U.S. group Sentry alleging corruption among top officials, saying such allegations would damage peace efforts in a nation which has been riven by war.
Sentry, a group co-founded by actor George Clooney and activist John Prendergast, said South Sudan's leaders on both sides of the civil war and their families had profited from the conflict.
"This sort of allegation can only jeopardise the pursuit of peace and stability in my country where mutual distrust and lack of authority are key factors of violence," a government spokesman said in a statement, expressing "deep concern."
"We will make sure that each of those allegations are challenged with a counter forensic and legal analysis of the shortcomings of this report," Ateny Wek Ateny, spokesman for the president's office, said.
Sentry said the report followed a two-year undercover investigation to look into the financing of African conflicts. It was released as the United Nations is threatening to impose an arms embargo against South Sudan's government.
Sentry said it had identified a network of international facilitators stretching from arms dealers in Ukraine to construction firms in Turkey, mining companies in Kenya, and Chinese investors involved in gambling and private security in South Sudan.
Spokesmen for President Salva Kiir and his rival, former deputy president Riek Machar, both denied allegations levelled against the two leaders when the report was released on Monday. Other senior officials were also named in the Sentry report.
South Sudan, which won independence in 2011, plunged into civil conflict in December 2013 after a long running political feud between Kiir and Machar, who are from different ethnic groups. Much of the fighting ran along ethnic lines.
A peace deal was signed in 2015 but proved shaky from the outset. Weeks after Machar flew back to Juba this year to return to his government post, fighting again erupted in July. Machar has since left the country.