In a statement, the mission said it was declaring the town a "no-go area" for UN staff.
Earlier this week, the special representative of the chairman of the African Union (AU) commission in the Sudan, Baba Gana Kingibe, expressed concern over the violence around Muhajiriya.
He said the town's security depended exclusively on the Sudan Liberation Movement/Army (SLM/A) and the Justice and Equality Movement (JEM), the two rebel groups that have clashed over control of the territory.
According to Kingibe, the latest hostilities began in March when JEM was forced out of Muhajiriya by the SLM/A. Consequently, JEM occupied Graida, 40 km from Muhajiriya, despite requests by the AU peacekeeping force in Darfur to relocate to some six km outside Graida.
On 3 June, the SLM/A attacked JEM positions in Graida with heavy bombardment and mortar bombs, which killed 11 people, wounded 17 others and burnt several houses, according to the AU Mission in Sudan (AMIS).
"Fighting is continuing in the countryside," a humanitarian source in South Darfur said.
He said tension between the two rebel groups had been high in the run-up to the resumption of peace talks on 10 June in the Nigerian capital, Abuja. He said the SLM/A had allegedly been seeking to "increase its influence" in Darfur as the latest round of peace talks approached.
The humanitarian source also said the SLM/A had been angered by the alleged defection of 80 of its fighters to the JEM and a claim that the rival forces had taken away three vehicles and three satellite telephones belonging to the SLM/A.
"These actions of the rebel movements, especially the relentless pursuit and attacks on JEM elements by the SLA with heavy civilian collateral damage, are unacceptable and condemned in the strongest terms," Kingibe said in a statement issued on 6 June.
"They constitute a serious breach of the Ndjamena Humanitarian Ceasefire Agreement and the arrangement which the government of the Sudan commendably respected by pulling its troops out of Graida and other locations, thereby paving the way for their demilitarisation and occupation by AMIS Forces," he added.
Earlier this week, the special representative of the Secretary-General for Sudan, Jan Pronk, expressed concern over the recent fighting, which he described as "irresponsible acts".
UNMIS said in a statement on 7 June that Pronk was "disappointed that these violations are taking place at a time when the international community and the African Union are exerting every effort to assist the parties in achieving a breakthrough during the upcoming round of talks".
In its latest update on the situation in Darfur and other parts of Sudan on Thursday, UNMIS listed a number of additional incidents, including the reported attack and robbery on 5 June of two commercial trucks on the Tawilla–Om Road in North Darfur by unknown armed men.
It said in West Darfur, armed tribesmen attacked the village of Gosmino on 4 June, abducted one individual and stole 43 domestic animals.
On 31 May, SLM/A representatives filed a complaint about an alleged attack on civilians at Fornu village in the area of Kutum by armed tribesmen.
The war in Darfur, which began in February 2003, pits Sudanese government troops and militias – allegedly allied to the government - against rebels fighting to end what they say is the marginalisation and discrimination of the region's inhabitants by the state.
An estimated 180,000 people have died and more than two million others have been displaced since the Darfur war began.