The Spanish and Slovenian ambassadors were called in on Monday, while the Belgian envoy was to be received on Tuesday, the ministry said in a statement.
The UN Human Rights Council voted Friday to send a team of international war crimes investigators to probe the deadly shootings. The three European countries were among 29 that voted in favour.
Only two of the council's 47 members, the United States and Australia, voted against the resolution, while 14 abstained, including Britain, Switzerland and Germany.
The text said the team should “investigate all alleged violations and abuses… in the context of the military assaults on large scale civilian protests that began on 30 March 2018, … including those that may amount to
Palestinians began protesting on the Gaza-Israel border on March 30 for the right to return to the homes their families fled or were expelled from in 1948, during the war surrounding the creation of Israel.
A total of at least 118 Palestinians have been killed by Israeli fire since then, according to authorities in Gaza, which is run by the Islamist movement Hamas.
No Israelis have been killed in that timeframe.
The protests peaked on May 14, the day the United States moved its embassy in Israel from Tel Aviv to Jerusalem. Tens of thousands protested on the Gaza border that day, with 62 killed by Israeli gunfire.
Israel says its actions are necessary to defend the border and stop mass infiltrations from the territory.
It accuses Hamas, with whom it has fought three wars since 2008, of seeking to use the protests as cover to carry out violence.