The UN Independent International Commission of Inquiry said it had found evidence that "Palestinian children have been deliberately targeted and killed by Israeli security forces".
In its Sunday statement, Al Jazeera said an "Israeli campaign of incitement has relentlessly spread false allegations and baseless accusations against Al Jazeera staff."
At least 1,012 Palestinians have been killed in Gaza since the ceasefire took effect on October 10 last year, according to the territory's health ministry.
The bodies of the two sisters, 4-year-old Zina and 14-year-old Lana, were sent to Shifa Hospital's morgue, where they lay shrouded in white hospital bags, surrounded by family members.
Israel has said it is continuing to operate against Hamas and allied militants in Gaza and has expanded the amount of territory it controls inside the strip.
