The assassination of Qari Zainuddin comes days after he revealed that their comrade was pursuing a US-Israeli agenda across the violence-wracked country.
Zainuddin, a 26-year-old rising tribesman who had called Mehsud "an American agent" was killed by a gunman in northwestern town of Dera Ismail Khan on Tuesday.
Zainuddin, who broke away from Mehsud, was also increasingly critical of Mehsud's use of suicide bombings targeting civilians.
In an interview with local media the defector said that Mehsud had established strong links with Israeli intelligence services, which were destabilizing the nuclear armed country. "These people (Mehsud and his men) are working against Islam."
Mehsud, a warlord in his late 30s, has claimed responsibility for dozens of devastating string attacks on both civilians and security forces throughout the feared region.
Insurgents have stepped up their attacks on civilian and religious centers in major cities across Pakistan, which has fueled anti-Taliban sentiments among the Pakistani people.
The US invaded Afghanistan more than seven years ago to allegedly eradicate insurgency and arrest Taliban and al Qaeda leaders.
The US invasion of Afghanistan in 2001 has resulted in the spread of violence into neighboring Pakistan. Taliban militants have turned the restive tribal belt between the two neighbors into a scene of daily violence.