President Kiir some of the generals form or join rebel groups with hope that they may be recalled and promoted in the army or government.
He made the remarks while briefing the army at the military headquarters in Juba.
President Kiir early this week retired dozens of police chiefs and is also expected to make a major reshuffle in the army.
South Sudanese President Salva Kiir has warned army officers against rebellion after leaving the military.
President Kiir said on Thursday that some of the generals form or join rebel groups with hope that they may be recalled and promoted in the army or government.
"If you want to rebel, you can rebel and remain there in the bush," President Kiir warned the soldiers at the military headquarters in the capital Juba.
In April, the President made similar remarks to the military warning that such intentions posed a major threat to the nation's peace and stability. He pledged to crush the rebellion.
Several army chiefs, who have been dismissed, have formed rebel groups intent on dislodging the government among them a former close ally of President Kiir, the ex-chief of general staff Gen Paul Malong.
South Sudan erupted in war in December 2013 after Mr Kiir fell out with his deputy president Riek Machar whom he sacked. The civil war, now in its fifth year, has since splintered.
Efforts to restore peace in the young country have been difficult as the many warring parties have failed to agree on a power-sharing agreement.
President Kiir early this week retired dozens of police chiefs and is also expected to make a major reshuffle in the army.
