The fighting started on Tuesday between the former rebel movement, which formed the administration in southern Sudan after signing a peace agreement in 2005, and the government.
"Unanimously, this is considered a major ceasefire violation," said Rhadia Achouri, spokeswoman for the United Nations Mission in Sudan (UNMIS). A "large number" of people were killed during the fighting, she added.
Other sources said hundreds of people were killed.
In New York, UN Secretary-General Kofi Annan expressed concern over the violence, saying the fighting constituted a serious violation of the security arrangements of the Comprehensive Peace Agreement (CPA).
The CPA, signed in Kenya in January 2005, also made the Sudan People's Liberation Movement/Army (SPLM/A) a partner in Sudan's government of national unity.
"The Secretary-General appeals to the government of national unity and the government of southern Sudan to make all possible effort to contain the situation, and expresses the hope that any differences in the area will be resolved peacefully," a statement from Annan's office on Wednesday said.
Some civilian UN staff were temporarily relocated to other areas in southern Sudan, it said.
A joint military delegation comprising high-level officers from the SPLA and SAF [Sudan Armed Forces], and the UNMIS Force Commander had arrived in Malakal to assess the situation, according to the statement.
Under the peace agreement, Malakal is policed by an integrated force of the SPLM and SAF.
This week's fighting started with a clash between SPLA soldiers and government-allied militias. It escalated when members of the militia sought cover in a government army garrison, which was then surrounded by the SPLA, prompting government troops to respond with artillery.
Situated on the banks of the Nile River, the area around Malakal falls within southern Sudan's oil-producing area. The two-decades-long civil war between the government and the SPLM/A war was fought, in part, over the south’s oil reserves.
The CPA provided for the creation of the autonomous government of southern Sudan led by President Salva Kiir Mayardit, who is also the vice president in the national unity government. It also granted southerners the choice to vote in a 2011 referendum on whether to remain united with northern Sudan or to secede and form their own nation.
nk/jn/mw
This article was produced by IRIN News while it was part of the United Nations Office for the Coordination of Humanitarian Affairs. Please send queries on copyright or liability to the UN. For more information: https://shop.un.org/rights-permissions