South Sudan gained independence from Sudan in 2011 under the terms of a peace agreement that ended civil war. Border conflicts, ethnic violence and disputes over oil have threatened the peace.
Johnson told the U.N. Security Council that violence in Jonglei, South Sudan's largest state, is a "major concern" for the U.N. Mission in South Sudan.
She said the government was committed to finding a peaceful solution but warned time was running out.
"The window for dialogue is closing and ... military operations may soon be launched," she said in a statement.
The International Committee of the Red Cross said this week that more than 60 people were treated following clashes in Jonglei in South Sudan. About half of those injured required emergency surgery.
Johnson said ongoing incidents of weapons proliferation in South Sudan had regional implications that required international attention.
"Every effort to mitigate that risk and keep South Sudan on a path to stability and prosperity will contribute to the stability of the whole region," she said.