Dawlat Waziri, spokesman for the Ministry of Defense, said the Haqqani network member was identified as Nooruddin who was killed in airstrike on Wednesday.
He said the airstrike was carried in the vicinity of Shahr-e-Safa city of Zabul province.
The anti-government armed militant groups have not commented regarding the report so far which comes as both the Afghan security forces and anti-government armed insurgents have stepped up attacks across the country.
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 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.
It is considered the most lethal insurgent group targeting the NATO-led coalition security forces and Afghan personnel in Afghanistan.
The US Department of State designated the HQN as a Foreign Terrorist Organization on September 7, 2012.