South Sudan's police force - made up of former rebels who fought Sudanese forces in the brutal 1983-2005 civil war - was thought initially to total around 52,000 men and women, police spokesman James Monday said.
"When the 16,000 names were checked in the database and the pay roll list they do not match," he said.
"We are yet to verify exactly where all the owners of these names are."
He added that so far 25,778 officers have been confirmed as real.
The minister says the clean-out will save the government US$9 million (A$11.54 million) a month.
The discovery follows United Nations-backed efforts to turn the ex-rebel-turned police into a more professional force, including weeding out rogue officers and clamping down on corruption.
The fledgling nation won independence in July 2011 but is still reeling from the impact of decades of war with Khartoum and is still suffering from rampant insecurity.
- AFP