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The ministry said two of the men, who it did not identify, were killed by Israeli fire east of Gaza City.
An AFP correspondent saw both bodies at the Shifa Hospital in Gaza City.
A third man, identified by the ministry as 29-year-old Abdul Salam al-Bakr, was killed east of Khan Yunis in southern Gaza.
The deaths brought the number of Palestinians killed since protests began on March 30 to 44.
154 other people were hospitalised for gunshot wounds and tear gas inhalation, Gaza's health ministry said.
As on previous Fridays, protesters gathered at five sites near the border fence, though numbers were down on earlier weeks.
Marchers are demanding the right to return to their homes seized by Israel in 1948.
Israel says that allowing the refugees in would mean the end of the Jewish state, and accuses Gaza's Islamist rulers Hamas of using the protests as a pretext for violence.
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