Rami Qahman, 28, died after being shot east of Rafah in southern Gaza and 37 other Palestinians were shot and wounded during the violence, the ministry added.
The border between the blockaded Gaza Strip and Israel has been rocked by deadly violence since March 30 when major protests backed by Hamas and clashes broke out along the frontier.
But for the second second consecutive Friday, clashes along the border were lower in intensity than in previous weeks, amid talk of a truce deal between Hamas and Israel. The deadly violence came as Palestinian civil servants formed long queues in Gaza yesterday to receive millions of dollars in Qatari-funded salaries, as part of efforts to ease tensions in and around the territory.
The funds were primarily to cover salaries of officials working for Hamas. The Israeli-authorised money transfer appeared to be part of a deal that would see cash-strapped Hamas end months of often violent protests along the border in exchange for Israel easing its decade-long blockade of Gaza.
At least 221 Palestinians have been killed by Israeli fire since the end of March, the majority shot during protests and clashes, while others have died in tank fire or air strikes. One Israeli soldier was killed by a Palestinian sniper.
Israel says its actions are necessary to defend the border and stop infiltrations and attacks, which it accuses Hamas of seeking to orchestrate.