The Hamas and Islamic Jihad movements claimed responsibility for the attack, and said in a joint statement that the perpetrator had disguised himself as a woman.
They also said he is a fighter wanted by Israeli forces and Palestinian police.
David Baker, an Israeli government spokesman, said: "This was a clear example of extremism and terrorism by those seeking to foil any prospects for advancing peace between Israel and the Palestinians."
Palestinian government officials were not immediately available for comment.
The attack is likely to further complicate efforts to forge a peace deal between Israelis and Palestinians in the West Bank.
Israel claims its continued military presence in the territory is necessary because Palestinian authorities are not yet capable of controlling armed groups.
Assailant escaped
The two guards were screening workers coming in when the assailant approached them, opened fire and then escaped, the military said.
Palestinian security officials in Tulkarem said soldiers moved into the West Bank in force after the attack and set up a checkpoint.
The small West Bank industrial zone where the attack took place, Netzanei Oz, contains five Israeli factories that employ Palestinians.
Israel's military regularly carries out arrest raids targeting Palestinians in the West Bank.
Israel has refused Palestinian calls to cease such operations and allow Palestinian security forces to take control.