Amnesty International and Human Rights Watch staff have not received permits to enter Gaza despite lobbying Israel and Egypt since the early days of the conflict, which began last month.
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They say the years-long Israeli ban on their international staff travelling to Gaza hinders their ability to investigate the violence, but Israel says neither group has the correct paper work needed to gain access to the Palestinian enclave.
Egypt's foreign ministry did not immediately comment why its own border with Gaza was apparently closed to the organizations.
The groups' inability to put international researchers and munitions experts into Gaza comes as Israel denies violations in its conduct of the war and is resisting a UN investigation into the conflict, dismissing it as a "kangaroo court".
"We're doing everything we can, both Human Rights Watch and us, to do all the documentation we can, both on the ground in Gaza and remotely. But not being able to have researchers there does create difficulties," said Amnesty worker Deborah Hyams, who said the group had just one local staffer on the ground.
Bill Van Esveld, an HRW Middle East researcher, told Reuters his group had two staff members in Gaza. "They're overwhelmed. There's so much to look into ... and physical evidence about the events there is disappearing as time goes by."
Six weeks of on-off fighting between Israel and Palestinian militants in Gaza has killed around 2,016 Palestinians - mostly civilians - as well as 64 Israeli soldiers and three civilians.
The UN's top human rights official last month said Israel appeared to be deliberately violating international law in a military offensive that hit homes, schools, hospitals, and UN shelters for Gazans fleeing the fighting.
Israel denies the allegations, pointing to warnings it sent to civilians to flee certain areas and countering that militants aimed rockets at Israeli civilians and operated from residential areas - something the UN says also may constitute a war crime.
An Israeli state body in charge of access to occupied Palestinian territories said it only granted permits to organizations registered at the ministry of social affairs.
"Because these organizations are not registered, they were informed that they can contact the public inquiries office in order to examine an individual application," said COGAT - a unit within the Israeli defense ministry.
HRW said it had contacted COGAT over the issue. Amnesty said it had not registered with Israel because it thought it would not be recognized as a humanitarian or development organization.
Both groups operate in the West Bank and Israel, but HRW has been denied entry to Gaza through Israel since 2006 and Amnesty since the summer of 2012. They say they have not received a clear explanation for the change in policy.
During an eight-day conflict in 2012, the organizations both entered Gaza through its border with Egypt. But that frontier has been closed for much of the recent fighting and the two groups said requests to Egypt for access via its Rafah crossing had not met with a clear response.
Cairo's relations with the Islamist Hamas movement that runs Gaza are strained, as are its ties with international rights groups that were highly critical of its 2013 crackdown on Islamist organizations.
Egypt last week turned away two top HRW staffers at Cairo airport as they were preparing to unveil a report on the mass-killing of protesters by Egyptian security forces last year.