The incident took place in the area of Kitkoot, 32 kilometres northwest of Khar, the capital of Bajaur tribal region.
"Up to five gunmen entered a mosque after evening prayers on Wednesday and opened fire on the local pro-government tribal elder Malik Juma Gul and his son, killing them both on the spot," senior local administration official Abdul Haseeb Khan told AFP.
He said Gul's two bodyguards sustained serious injuries in the attack.
Another senior local official, Shah Naseem Khan, also confirmed the deaths.
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The incident came hours after gunmen ambushed a car of local pro-government fighters in Kooza Bandi village in the northwestern Swat Valley, and killed three people.
Pro-government militias rose up in reaction to the brutal reign of Taliban and Al-Qaeda linked militants in the tribal regions after 2007.
Bajaur is one of seven semi-autonomous districts that make up the tribal regions branded by the US as the most dangerous place on earth, where Pakistan's military has launched a series of operations against homegrown insurgents in recent years.