The South Sudanese government has reported tracing its missing Sh1.03 billion to accounts at Ecobank, Kenya Commercial Bank and Co-operative Bank of Kenya.
These are linked to Lt Gen Thomas Cirillo Swaka - former SPLA Deputy Chief of Staff in charge of logistics, and his kin Fueni Cirillo.
An Ecobank statement seen by the Star shows transactions on the money after it was reported missing from the South Sudan government this month.
These were for account 0040025032685901 belonging to Fueni.
Paul Awan, chief of general staff, said the cash went missing after Swaka quit his job and defected from Sudan People's Liberation Army.
A letter dated February 9 shows that Awan asked Renish Omullo, a special envoy in charge of Germany international and regional affairs, to trace and return the cash which was transacted in US dollars.
Renish wrote to Foreign Affairs Cabinet Secretary Amina Mohamed on February 10 requesting that bank accounts held by Swaka and Cirillo be frozen.
Swaka is described in the letter, also seen by the Star, as a former SPLA officer and fugitive in Kenya who stole more than $10 million.
"This office is under instructions from the Office of the President, Government of South Sudan to kindly request you to facilitate a freeze of these accounts and recover the money back to Bank of South Sudan A/C name - Military Strategic Division; A/C no - (USD) 0026921002607," Renish says in her letter.
"However this letter has not gone through our embassy in Nairobi because of the sensitivity of the matter and conflict of interest at the embassy."
Renish said the money had already been secured and would be rerouted back to South Sudan.
Reached for comment, Ecobank said in a statement: "We do not have such an account, neither do we have an official request on the same."
Co-operative Bank and KCB were not immediately available for comment while officials at the Foreign Affairs ministry referred the Star to the Interior ministry.
In his resignation, Gen Swaka accused President Salva Kiir and SPLA leaders of abuses and pushing the tribal agenda in the country.
He becomes the second highest-ranking officer to resign after Gen Bapiny Monytuil since clashes erupted between government soldiers and opposition fighters in July 2016.
A report revealed in September last year that South Sudan's political and military elite had siphoned money from their country and bought expensive assets in Nairobi and other capitals within East Africa.
Among the many details outlined in the report are pictures of luxury villas, said to be owned by politicians and generals in Kenya, Uganda, Ethiopia and Australia.
Read The Sentry's investigative report: War crimes shouldn't pay: Stopping the looting and destruction in South Sudan