Maulana Hami ul Haq, son of Maulana Samiul Haq, said that his father was resting in his room when he was attacked with a knife.
Maulana Samiul (82) was the head of the Islamic religious seminary Darul Uloom Haqqania in Khyber Pakhtunkhwa's Akora Khattak town.
Some reports say he was killed in a knife attack, while others say he was shot after gunmen opened fire on his vehicle.
Samiul Haq was the chief of Jamiat Ulema-i-Islam and died in an assassination attempt, news agency PTI reported.
The prime minister's Pakistan Tehreek-e-Insaf (PTI) entered into a pre-election alliance with Haq's JUI-S, although the two later parted ways before Pakistan's July general vote, which Khan's party swept.
He has twice been a member of the Senate of Pakistan from 1985 to 1991 and again from 1991 to 1997.
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A divisive figure, Haq was known as the "Father of the Taliban".
Maulana Yousuf Shah, a party spokesman, said unidentified attackers killed him in his residence and fled the scene. The army chief also extended his condolences to the bereaved family.
Prime Minister Imran Khan, who is now in China for an official visit, said the country had been deprived of an important religious leader whose services would always be remembered. In a statement from Beijing, where he is now on visit to China, the Prime Minister directed to investigate the incident and bring the perpetrators to justice. "He had been ill, and was a heart patient", said Hamidullah.
However, other reports from Pakistan said Sami ul Haq was stabbed to death.
He was a religious scholar and former Senator. He said that Haq's services would always be remembered.
Minister of State for Interior Shehryar Afridi has also condemned the assasination.