Another peacekeeper was injured in the fighting Thursday in Akobo Town, the U.N. mission said in a statement. The bodies of the dead were brought to Juba.
The U.N. troops in Akobo are from India, officials said.
The attackers were young men from the minority Lou Nuer group, the U.N. said.
UNMISS, the U.N. Mission in South Sudan, said it sent four helicopters to rescue personnel from the Akobo base in Jonglei state, the New York Times reported.
U.N. Secretary-General Ban Ki-moon said in a statement he was "appalled" to learn of the attack on the Akobo base and called on government and opposition forces to respect the rights of civilians and ensure their safety and security.
"UNMISS is doing everything it can, within its means and in a very fluid situation, to protect civilians, as well as United Nations and international personnel on the ground," Ban said. "There are indications that civilians may have been killed and wounded in the attack, but this remains to be verified. Should these reports prove true, those responsible must be held accountable for their crimes."
President Obama, in a letter to Congress Thursday, said 45 U.S. troops were deployed to South Sudan to support "the security of U.S. personnel and our embassy" and would remain in-country "until the security situation becomes such that it is no longer needed."
In a statement Obama, noting South Sudan elected to become a country in 2011, now "stands at the precipice."
"Too much blood has been spilled and too many lives have been lost to allow South Sudan's moment of hope and opportunity to slip from its grasp," the statement said. "Now is the time for South Sudan's leaders to show courage and leadership, to reaffirm their commitment to peace, to unity, and to a better future for their people."
The country has been in turmoil since Sunday when President Salva Kiir accused soldiers loyal to former Deputy President Riek Machar of a coup attempt, which Machar has denied.
Reports indicate hundreds of people have been killed in the fighting since Sunday.
The U.N. mission said it has has more than 6,800 troops and police in South Sudan.
"Violence is spreading and could spread even further and we need all South Sudanese leaders and political personalities now to immediately appeal [for] calm and call on their supporters to suspend hostilities," Deputy Secretary-General Jan Eliasson said during a news conference at U.N. headquarters in New York. "Political dialogue is the only way to prevent further escalation."
Britain sent a second plane to Juba, South Sudan's capital, Friday to evacuate British nationals, the Wall Street Journal reported. Britain sent a first plane Thursday.
At the time of the assault, the Akobo base housed 43 Indian peacekeepers, six U.N. police advisers, two civilians and about 30 South Sudanese who had sought refuge from the fighting in the area, the United Nations said. The mission said 34,000 people had taken refuge at its facilities throughout the country.
In Geneva, Switzerland, U.N. High Commissioner for Human Rights Navi Pillay said an estimated 20,000 people, mainly women and children, were camped at a U.N. facility in Juba. Others are reported to be fleeing for fear of attack by rival groups.