The group has been behind many of the co-ordinated gun and bomb attacks on Afghan and Nato forces in recent years.
Afghan officials say Anas Haqqani, the son of the network’s founder, was arrested with commander Hafiz Rashid.
Haqqani leaders were thought to be based in Pakistan’s tribal areas but reports say many fled to Afghanistan after a recent army offensive there.
The ageing founder of the Haqqani network, Jalaluddin Haqqani, is still thought to be in Pakistan. His son, Sirajuddin Haqqani, is thought to be in de facto control of the organisation.
Afghan NDS intelligence officials say that Anas Haqqani and Hafiz Rashid were arrested late on Tuesday in Afghanistan. They added that Anas Haqqani had played an important role in the network’s strategy and fund-raising..
Intelligence officials told BBC Afghan that Anas Haqqani had particular skills in computing and was the main force behind the network’s social media propaganda efforts. Hafiz Rashid was described as a senior military commander who trained and equipped suicide bombers.
“We hope that these two arrests will have direct consequences on the network and their centre of command,” NDS spokesman Haseeb Sediqi told the AFP news agency.
Late last year, another son of Jalaluddin Haqqani was shot dead near the Pakistani capital, Islamabad. Nasiruddin Haqqani, who was in his early 30s, had been the group’s chief fundraiser.
The network – which has links to al-Qaeda and the Taliban – carried out a series of high-profile attacks against foreign and Afghan troops since US-led forces drove the Taliban from power in 2001.