Israeli forces fired on a vehicle with the Palestinian men inside near the Surra military checkpoint, west of Nablus, Palestinian news agency Wafa reported.
The Israeli army said that "gunmen opened fire" at a checkpoint near the Jit junction, adding the Israeli forces "responded with live fire", according to an army statement.
"Three armed gunmen were neutralised during the exchange of fire and an additional armed gunman surrendered himself to the forces," the statement said, noting none of the Israeli forces were wounded in the alleged attack.
The head of the Palestinian National Council, Ruhi Fattouh said that the Israeli government must be held accountable for the killing of the Palestinian men.
"The occupation forces erect death barriers at entrances to Palestinian towns to kill citizens in cold blood under false allegations to justify their daily field executions," Fattouh said in a statement carried by Wafa.
Fattouh said that the repeated executions at military checkpoints are a clear indication that the occupation forces "have explicit instructions to kill" from the Israeli government.
Sunday's killings took place a short distance from an illegal Israeli settlement.
The head of a Jewish settler group, Yossi Dagan, praised the occupation forces over the killings, according to AFP.
"We will continue to live and build here in Samaria and the entire region," he said, referring to the Palestinian territory occupied by Israel since 1967.
Violence has worsened in the occupied West Bank since Israeli Prime Minister Benjamin Netanyahu returned to office in December in a governing coalition with ultra-Orthodox Jewish and extreme-right allies.
Rights groups have frequently urged authorities in Tel Aviv to stop the "unlawful killings of Palestinians by Israeli forces", saying they amounted to "extrajudicial executions".