Israel said its troops returned fire at the armed Palestinians but did not have details on casualties.
The soldiers shot at armed Palestinians, the military said, but had no information on the condition of those hit.
"You can't allow armed Palestinians running inside the village while your forces are inside," the commander said.
"The Palestinian police must ensure that no armed Palestinians can reach the crossing points."
Israeli troops killed two armed Palestinians and a Palestinian teenager was shot dead.
He did not discuss the presence of armed Palestinians.
Yesterday you saw an armed Palestinian through cross hairs, and today you're driving with him to make peace.
The Israeli military confirmed that its troops had hit a number of armed Palestinians.
The Israelis also relaxed the rules under which their soldiers may fire at armed Palestinians.
They know that if they pick up a gun, there are armed Palestinians facing them.