A spokesman for the ministry said in a statement that the man, whose identity was not yet known, was killed during protests east of Gaza City, AFP reported on Friday.
More than 100 other people were wounded, the spokesman said.
Palestinians have been demonstrating along the border for months in often violent protests that have seen at least 184 Palestinians killed by Israeli fire since March 30.
Friday’s demonstrations were reportedly more ferocious than in recent weeks.
The clashes in Gaza reached their peak on May 14, the eve of the 70th anniversary of Nakba Day, or the Day of Catastrophe, which coincided this year with Washington's relocation of the US embassy from Tel Aviv to occupied Jerusalem al-Quds.
On June 13, the United Nations General Assembly adopted a resolution, sponsored by Turkey and Algeria, condemning Israel for Palestinian civilian deaths in the Gaza Strip.
Gaza has been under Israeli siege since June 2007, causing a decline in living standards as well as unprecedented unemployment and poverty.
Israel has also launched several wars on the Palestinian sliver, the last of which began in early July 2014 and ended in late August the same year. The Israeli military aggression killed nearly 2,200 Palestinians and injured over 11,100 others.