Aljazeera's correspondent in Kandahar reported that the clashes started on Friday in the Ghirshak area of the Helam Province, about 80 km west of the city.
Fighting has continued well into the night.
The fighting between supporters of Mulla Amir Dad Mohammed Khan and Mulla Idris have killed ''tens of people'', eyewitnesses told Aljazeera.
US force are reported to have headed to the region, in an attempt to the diffuse the situation, the correspondent added.
Mulla Amir Dad Mohammed Khan, the region's security chief confirmed to Aljazeera that the clashes had taken place, but he denied that 30 people had been killed, saying that the number of fatalities was much lower.
US Central command told Aljazeera.net that they knew nothing about the incident and had no information about US troops being sent to the Kandahar area in response to the violence.
Both commanders are allied to the Afghan president Mohammed Karzai, and are said to have been using heavy weaponry.
Fighting has erupted 80km west
The Pakistani news agency AIP reported that four civilians were killed in the clashes.
Another eyewitness told the news agency that as many as 45 people may have been killed in the violence.
In a separate incident, an Aljazeera correspondent in Kabul has reported that a number of Taliban fighters have occupied the Wara Bor provisional headquarters in Konar province, east of Afghanistan.
The fighters forced the employees to sign an undertaking to abstain from working with the government, in return for their release, the correspondent said.
Fighters held employees inside the building for two hours, and then set the building ablaze.
US forces reached the scene, but were ambushed, the correspondent added.
“Taliban operations have escalated in eastern Afghanistan, particularly Konar province, where the fighters conduct almost daily attacks against Afghani troops and US forces,” the correspondent said.