Four of the dead were killed during a raid on Jenin refugee camp, the ministry said on Wednesday.
Two others were killed in Jericho and the Gaza Strip, where a man was shot dead along the border fence with Israel.
Zaghram Al Akars, 19, was shot in the head during a raid on the Aqabat Jabr refugee camp in Jericho, while Atta Yasser Muta, 25, died on Wednesday morning of wounds sustained in the Jenin raid.
Dozens of others were wounded in Jenin, the refugee camp that was partially destroyed in July, when Israel carried out its largest raid there in two decades.
Thirteen Palestinians, including several children, were killed in that raid, which left several parts of the camp reduced to rubble.
The Israeli army confirmed troops were operating in Jenin on Tuesday evening and said a drone had struck the main refugee camp.
The camp has suffered the highest death toll in Palestine this year, passing last year's record fatalities, which marked the highest toll since the Second Intifada.
“The ongoing Israeli aggression against our people in Gaza, Jenin and other Palestinian cities will bring violence and escalation to the entire region,” said Palestinian Deputy Prime Minister Nabil Abu Rudeineh.
It comes as tensions mount in the blockaded Gaza Strip, where youths havestaged protests on the border with Israel for several days.
Youssef Radwan, 25, was shot in the neck and died at the border, Gaza health officials said.
He was the first person to be killed by Israeli fire in Gaza for several months.
Israel said it fired at “rioters” on the border who detonated explosive devices. It later said it was closing the border following the incident.
At least 236 Palestinians have been killed so far this year in incidents linked to the conflict.
The violence has also led to the deaths of 32 Israelis, a Ukrainian and an Italian, according to an AFP tally based on official sources on both sides.
Israel's right-wing government has pledged to crack down on Palestinian attacks. Members of the cabinet have also encouraged settler violence in Palestinian communities, further inflaming tensions.