"I have so far received seven bodies of protesters," said a doctor from Herat's central hospital, who did not want to be identified.
Protests erupted in the provincial capital in the west of the country after President Hamid Karzai sacked powerful local leader Ismail Khan as Herat governor on Saturday.
On Sunday several hundred of Khan's backers, shouted anti-Karzai and anti-US slogans before setting fire to the office of the United Nations High Commissioner for Refugees and the UN Assistance Mission in Afghanistan (UNAMA).
On Saturday night hospital officials and witnesses said at least two people were killed in clashes with US and Afghan forces.
The US military said there were no casualties.
The protest escalated despite the presence of hundreds of Afghan and US troops deployed to keep order in the city.
The protesters broke into the UNAMA compound where they hurled stones and set fire to at least one UN vehicle after chanting slogans outside for about half an hour, said UN spokesman Manoel de Almeida de Silva.
He said about 10 UN staff were in the compound at the time, but he had no reports of injuries.
US Ambassador Zalmay Khalilzad, a close confidant of Karzai, said on Saturday he had spoken to all concerned, including Khan, and urged them not to take any action that might threaten security.
The protestors chanted anti-Karzai
This was echoed by the United Nations, whose Special Representative Jean Arnault said in a statement released before Sunday's violence that the replacement of the governors had boosted the chances of peaceful elections next month.
"The United Nations calls upon all concerned parties to put first the interest of the country and the stability of the western provinces," he said.
In launching his campaign, Karzai told supporters he had no intention of forming a coalition government if he won the election.
Hours later, a statement from his office said Khan had been "promoted" to minister of mines and industry, a move widely seen as sidelining the regional strongman ahead of upcoming general elections.
Sayyid Muhammad Khairkhwa, currently ambassador to Ukraine, was named as Khan's replacement.
The silver-bearded Khan, who earned the nickname "Lion of Herat" for his struggle against the Soviet occupation in the 1980s and had twice previously declined cabinet positions, said he accepted his replacement, but turned down the new post.
He said he would remain in Herat as a "private citizen".
Relations between Khan and Karzai have soured since Khan's son, Civil Aviation Minister Mirwais Sadiq, was killed in a clash with government troops in March.
Herat has also been the scene of recent bitter fighting between forces loyal to Khan and an old rival, Aman Allah Khan, which diplomats said had helped erode the governor's power base.
The fresh violence will be a concern for US President George Bush who is hoping a peaceful Afghan election will offset negative publicity from Iraq and provide an incentive for his own re-election chances in November.