The report concluded that explosion led to the death of Meissar Abu Megteg, the mother, and four of her children, aged one to five.
The findings are at odds with other reports of the incident, including from Ahmed Abu Megteg, who witnessed the explosion that killed his wife and children.
He told Al Jazeera there were no fighters or fighting in the area.
"I did not see any fighters, There were no fighters around here ... no fighting, neither from the Arabs or the Israelis," he said.
Al Jazeera's Jacky Rowland, reporting from Jerusalem, said there has not been any "significant change" to Israeli army rules of engagement following the Beit Hanoun incident.
"The Israeli army generally uses the argument that this is a conflict zone. That the Israeli soldiers are operating in a conflict zone against armed Palestinians and therefore basically the rules of war apply," she said.
"We are likely to see pretty much the same outcome as and when the Israeli army does release its findings".
B'Tselem, the Israeli human-rights organisation, also contradicted the official report, saying on Wednesday that its own investigation showed the Palestinian family had been killed by a second missile rather than a secondary explosion.
"About a minute later, the aircraft fired a second missile, this one at a fourth armed man, who was about 15 metres from where the first missile landed, and about one metre from the gate of the Abu Megteg family's house," the group said in a statement on its website.
"This [second] missile killed the fourth armed man and the five members of the family."
Sarit Michaeli, from B'Tselem, told Al Jazeera that the group was calling on the Israeli army to release footage of the missile attack, filmed by the drone that fired the missiles, in order to build up a complete picture of the incident.
Ahmed Abu Megteg, witnessed the explosion
that killed his wife and children [Reuters]
But she stressed that ultimately the question was whether a missile should have been fired at all.
"The main issue is whether a missile should have been fired at a militant who is standing right on the doorstep of a family - of a residential home in Gaza - in a very densely populated area."
The Gaza-based Palestinian Centre for Human Rights also differed from the Israeli report, saying the family had been killed by shrapnel from the second missile.
"The shrapnel destroyed the door of the house and flew inside, where Meissar Abu Megteg, 40, and her six children were eating breakfast just two metres from the door," the organisation said.
Israel said earlier that it regretted the family's death but criticised Hamas for allowing its fighters to operate in civilian areas.
Meanwhile, on Wednesday an Israeli air raid killed one person and wounded three others in the Gaza Strip.
The attack in Rafah in the south of Gaza targeted a metal workshop.
Israeli officials say the man killed was a Palestinian fighter. A child has also been injured.