The ministry announced the death of Imad Abu Rashid, 47, who "was killed by the Israeli forces, after being shot in the abdomen, chest and head".
In a later statement, it announced the death of Ramzi Sami Zabara, 35, "from a critical wound by Israeli bullets in the heart, in Nablus".
Local sources said that the two men, who hailed from Askar camp near Nablus, were members of the Palestinian Security Forces and were killed during an armed clash with the Israeli army at Huwara, south of Nablus.
The incident is the latest in a deadly week in Nablus, where Israeli forces have conducted regular raids and imposed tight restrictions on movement.