President Salva Kiir made the comments Tuesday in a meeting at the army's general headquarters in Bilpam where he addressed thousands of soldiers ranging from junior officers to the chief of general staff, the Sudan Tribune reported.
It was his second meeting with the army following his return from a mission to Uganda amid rumors of a plot to topple him.
Fears of a coup by unknown forces surfaced when several of South Sudan's top leaders were out of the country.
Kiir was visiting Kampala, Uganda, with his defense minister and the chief of general staff, while Vice President Riek Machar was at the United Nations in New York.
Majak Agoot, the deputy minister of defense, was in charge of the army while his superiors were out of the country.
Kiir said the coup rumors implicated Maj. Gen. Simon Gatwec Dual, who is in prison, as having links to rebels in the state of Jonglei.
A member of the Lou-Nuer community in Jonglei said Dual had no involvement with any plots and that he had no connection to rebel groups in the area. He charged the general was being used as a scapegoat.