The United Nations is investigating reports of mass killings since violence began spreading after a Dec. 15 fight among the presidential guards that pitted soldiers from Kiir's Dinka ethnic group against those from the Nuer ethnic group of Machar.
"It's very important to underline this is a political struggle," Johnson said, stressing that there is "multi-ethnic representation on both sides."
The United Nations estimates "well over a thousand killed" in the 11 days of fighting, Johnson said.
Although the capital, Juba, is now calm, fighting appears to be expanding, stretching the limits of humanitarian workers and aid agencies. The U.N. humanitarian office said aid agencies need $166 million to save lives amid the continuing violence.
The money will be used to provide water, sanitation, shelter, food and health care, plus protection for vulnerable people, the office said in a statement.
Some 58,000 people have taken refuge in and around U.N. bases in South Sudan, and more than 92,000 have fled their homes as a result of fighting, according to the U.N.
The U.N. Security Council last week voted unanimously to beef up its peacekeeping force in South Sudan from about 8,000 troops and police to nearly 14,000 and send attack helicopters and other equipment.
Johnson said she expects some military reinforcements and equipment to start arriving in 48 hours to help protect civilians seeking refuge at U.N. bases.
Before the 2005 peace agreement, the region that is now South Sudan fought decades of war with Sudan. One of the world's least developed countries, it still has pockets of rebel resistance and sees cyclical, tribal clashes that result in hundreds of deaths.
Muhumuza reported from Kampala, Uganda. Associated Press writers Edith M. Lederer and Cara Ana contributed to the report from the United Nations.