Some 800 tribesmen watched the executions by the Lashkar-i-Islam (Army of Islam) group on Wednesday in the Bara region of the Khyber tribal district on the border with Afghanistan, they said.
The trio were tied up with ropes, and tribal elders and other men gathered at a patch of open ground and stoned them. Two masked members of the hardline group then shot them with Kalashnikov rifles, witnesses said.
The killings are likely to fuel concern about the "Talibanisation" of parts of Pakistan and the introduction of Islamic Sharia law, particularly in the tribal areas and in North West Frontier Province bordering Afghanistan.
"The Lashkar-i-Islam men caught them and after investigations it was proved that they were guilty of adultery," a group member said on condition of anonymity.
Members of the religious group, led by cleric Mangal Bagh, raided a house on Monday and abducted the three after local residents suspected them of "illicit" activities, local residents said. The victims were named as Allah Noor and Shahzad while the woman was identified as Taslima.
The local administration said it did not intervene in the situation as the restive tribal agencies are semi-autonomous and Pakistani laws do not apply.
"We had reports about the killings, but we do not interfere in the matters related to tribal customs and traditions," a tribal administration official said.
The killings come less than two months after two lovers were tied to trees and stoned to death for adultery by angry relatives in Donga Bonga village in central Punjab province, in a so-called "honour killing".