Nasiruddin was killed by two gunmen riding a motorcycle when he was returning home from a mosque in Barakahu area late last night, the leaders said.
"I can confirm that Dr Nasir has been martyred," a militant, who previously worked with the Haqqani network in North Waziristan, was quoted as saying by The Express Tribune.
There was no independent confirmation of the report. Islamabad Police sources denied knowledge of the incident.
The militant said Nasiruddin's body had been sent to Miranshah in North Waziristan Agency yesterday for burial.
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Nasiruddin, the eldest son of Haqqani network founder Jalaluddin Haqqani, was involved in "dialogue-related affairs" of the group. According to the US, he was a key financier and emissary of the dreaded network. Three more of Jalaluddin's sons have also been killed.
Born in Paktika province of Afghanistan, Nasiruddin was put on the UN Security Council's sanctions list of individuals subjected to an assets freeze, travel ban and arms embargo after the 9/11 terror attacks.
The Haqqani network is considered the most dangerous Taliban faction in Afghanistan. The Haqqanis have been blamed for devastating attacks on the Afghan government, US and Nato forces and the Indian Embassy in Kabul.