"It is with great regret that we have learned about the martyrdom of Nasiruddin Haqqani, may Allah accept him," the conservative Islamic movement said.
The Express Tribune, a Pakistani newspaper, reported he was killed Sunday when gunmen on a motorcycle shot him 26 times as he returned from a mosque.
The Haqqani militant network is considered the most violent of the Taliban factions fighting in the region. The movement was founded by the slain leader's father, Jalaluddin Haqqani.
"We strongly condemn this cowardly action of the defeated enemy and remind them that such terrorist activities will never negatively affect the strong and broad active jihadi process," the Taliban statement read.
The U.S. military said last year Badruddin Haqqani, another senior leader, was killed by a missile fired from an unmanned drone over Pakistan. He was suspected of coordinating attacks with the Taliban inside Afghanistan.