Israel has ordered that fuel deliveries into Gaza be halted, citing violence against Israeli soldiers and citizens by Palestinian protesters.
At least 204 Palestinians have been killed by Israeli fire in Gaza since March 30, when Palestinians in the Gaza Strip began holding nearly daily protests near the buffer zone.
Thousands of Palestinians marched on Friday after convening at five locations along the fence, with Israeli troops responding from across the barrier with tear gas and gunfire.
It said four died along the frontier east of Al-Bureij in central Gaza, two east of Gaza City and one near Rafah in southern Gaza. A Palestinian succumbed to his wounds later, Gaza health officials said.
Gaza medics said that, in addition to the six dead, around 140 others were wounded.
On Friday, a bomb was detonated along the fence and a number of Gazans entered into Israel, according to IDF spokesman Lt. Col. Jonathan Conricus, who tweeted "some 20 terrorists crossed through the hole created by the IED, about 5 assaulted the IDF position and were repelled".
One Israeli soldier has been killed.
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It said they planted an "explosive device" which blew up and "set the security fence on fire".
About 600,000 Israelis live in over 230 illegal settlements built since the 1967 Israeli occupation of the Palestinian territories of the West Bank and East Jerusalem al-Quds. An Israeli soldier was killed over the same period.
Addressing the unrest, Israeli Defense Minister Avigdor Lieberman chose to cut Qatari fuel shipments into the Gaza Strip in response to the mass protests.
The Israeli army said approximately 14,000 people had gathered at various sites along the border.
Israel accuses the enclave's rulers Hamas of leading the protests and using them as a cover for attacks.
The Palestinian leadership has rejected any future cooperation with United Nations special coordinator for Middle East peace Nickolay Mladenov, informing the worldwide body that he is "no longer acceptable" because he has "gone beyond his role" in attempting to broker agreements between Israel and Hamas.