"We haven't killed Burhanuddin Rabbani and this has been said many times by the spokespersons of the Islamic Emirate," Sirajuddin Haqqani told BBC in an interview, his first public utterances in years.
Sirajuddin also said his network, blamed by United States military officials for a string of high-profile attacks on American interests in Afghanistan, was not linked to Pakistan's ISI.
Former US military chief Admiral Mike Mullen had branded Haqqani network as a "veritable arm" of ISI, used by the spy agency to wage a proxy war in Afghanistan.
But the Haqqani network chief said that the 'Islamic Emirate', the name given to the Taliban government when they assumed power in Afghanistan in 1996, was behind "the attack on US embassy, Nato headquarters and other attacks in Kabul, which he said were ordered by a military council of Taliban.
Vowing what he called the "game being played by the West... is close to an end", Sirajuddin said, "In every operation we get the order, planning and financial resources from the Emirate's leadership and we act accordingly."
He pledged loyalty to Taliban chief Mullah Omar, saying "he is our leader and we totally obey him."
Afghan officials have blamed Taliban for the September 20 assassination of Rabbani by a turban bomber, saying the killer was a Pakistani and the plot had been hatched in Quetta in Balochistan, where top Taliban council is based.