The aide confirmed rumors that had been circulating in Juba for several days, the Sudan Tribune reported. The official, who didn't want his name used, described the theft as a "big embarrassment."
"It was shocking news to me when I woke up one morning to learn that millions in cash money which was stored in the president's office had gone missing," he said.
The official couldn't explain to the newspaper why the money was kept in the president's office in cash and not in banks.
South Sudan, which became independent from Sudan in 2011 after a referendum, has been dogged by accusations of corruption.