She said steps were taken to ensure "fighting factions were aware these flights were a humanitarian mission".
Washington was forced to give up an evacuation effort Saturday, after a US military aircraft sent in to airlift Americans came under fire with four soldiers wounded.
Psaki said some 380 US officials and citizens as well as about 300 citizens of other countries have been airlifted so far to Nairobi, capital of Kenya and other places on four chartered flights and five military aircraft.
President Barack Obama deployed 45 US troops to South Sudan last Wednesday to protect American citizens and property.
Fighting broke out in Juba Dec 15 between forces loyal to President Salva Kiir and his former deputy Riek Machar, who was removed from office in July. Armed conflicts are spilling over to other parts of the country and setting off reportedly ethnic violence.