Fares Hafez al-Sersawi, 14, and 24-year-old Mahmud Akram Mohammed Abu Samane, both died after being shot in the chest during demonstrations east of Gaza City, ministry spokesperson Ashraf al-Qudra said.
Hussein al-Rakab, 28, died after being shot in the head near Khan Yunis in the south of the Gaza Strip, Qudra said.
Palestinian teen dies from wounds in Gaza unrest: ministry
A further 376 people were wounded, including 126 who had been shot, according to health ministry figures.
Seven were in a critical condition including a medical volunteer. The Israeli military said around 20,000 Palestinians took part in Friday's protests at numerous points along the Gaza border, continuing a series of demonstrations which began in March.
Grenades, explosives and stones were launched at Israeli soldiers posted behind the barrier which separates Gaza from Israel, the military said.
Israeli forces responded with live fire and an aircraft also carried out two strikes in Gaza, the military said.
The armed forces said it could not immediately comment on the circumstances surrounding the deaths of the Palestinians.
Border protests have been ongoing since March 30 in the Gaza Strip, which is run by Hamas and has been under a crippling blockade by Israel for more than a decade.
Demonstrators are calling for the right for Palestinians to return to their former homes, from which their families were expelled or fled during the 1948 war surrounding the creation of Israel.
The rallies frequently turn violent on the closely-guarded frontier.
At least 198 Palestinians have been killed by Israeli fire in Gaza since March 30, while one Israeli soldier has been shot dead by a Palestinian sniper.
Israel says its actions are aimed at protecting its territory, soldiers and civilians who live close to the Gaza border.
The army accuses Hamas of orchestrating the demonstrations - including the participation of children - as cover for its hostile activities.
Palestinian activist honoured with Real Madrid jersey
Israel has fought three wars with Hamas since 2008 and considers the group a 'terrorist' organisation.
Following a period of relative calm, there has been a resurgence in mass protests in recent weeks.
The lack of progress in diplomatic efforts and continued disagreements between rival groups in Gaza have prompted fears of a new escalation of violence in the enclave.
Gaza's two million residents endure dire living conditions including a shortage of safe drinking water and regular power cuts.
The World Bank said last month Gaza's economy is in "free fall", as cuts to aid and salaries add to the damaging impact of the blockade.
COMMENTS (1)
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ