Maulana Samiul Haq, 81, was attacked inside his house in the city of Rawalpindi, near the capital, Islamabad, by two knife-wielding assassins, his son Hamidul Haq said on Friday.
JUI-S's Peshawar president also confirmed the chief's death following an assassination attempt in Rawalpindi.
Sami-ul-Haq, 80, was stabbed to death in his bed on Friday, his son Hamidullah told local television news channel ARY by telephone. "It was really sad to hear the news of martyrdom of Maulana Samiul Haq", Nawaz said, praying to the Almighty to have mercy on Pakistan.
Sami ul-Haq, who was in his 80s, was known as the father of the Afghan Taliban due to the huge influence and respect he enjoyed among the leaders of the militant group.
He was regarded as the "Father of the Taliban" because of the relationship between a student (Talib) and Teacher is a relationship of Father and Child, and had close ties to Taliban leader Mullah Mohammed Omar.
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His JUI-S party was an ally of the ruling Pakistan Tehreek-e-Insaf (PTI) party headed by Prime Minister Imran Khan. He said Sami-ul-Haq was a great religious scholar and leader.
Maulana Sami, said to be around 82 years old, was the head of the Darul Uloom Haqqania seminary in Khyber Pakhtunkhwa's Akora Khattak.
Within Pakistan, Haq was considered a hardline right-wing religious cleric, but his party contested elections, rather than outright backing armed struggle against the state, as was undertaken by the Pakistani Taliban.
Khan, now on an official visit to Beijing, condemned the killing and ordered an investigation, his office said in a statement.
Samiul Haq was also a founding member of Muttahida Majlis-e-Amal. Condemning this tragic incident, he expressed sympathy with the bereaved family.