According to the local security officials, the commander was identified as Kernel and was involved in insurgency activities for the Haqqani terrorist network.
Provincial police chief Faizulllah Ghairat confirmed that Kernel was killed during a clash with the Afghan forces in Sapera district.
He said Kernel was originally a resident of Khost province and was involved in major destructive activities as he was fighting for the Haqqani network.
Ghairat further added that two companions of Kernel were wounded and another was arrested by the Afghan forces.
The anti-government armed militant groups have not commented regarding the report so far.
The Haqqani terrorist network is accused of staging numerous cross-border attacks from their base in North Waziristan, including the 19-hour siege at the US Embassy in Kabul in September 2011.
Haqqani network was formed in the late 1970s by Jalaluddin Haqqani. The group is allied with al-Qaida and the Afghan Taliban and cooperates with other terrorist organizations in the region.
The US Department of State designated the HQN as a Foreign Terrorist Organization on September 7, 2012.