Some bodies inside the mass graves in Gaza had their hands tied together, the United Nations Office of the High Commissioner for Human Rights (OHCHR) alleged in a statement calling for an investigation into the situation.
At least 238 bodies were discovered outside Nasser Hospital in Khan Younis, while a similar site was found in a similar site near Al-Shifa Hospital in Gaza City.
The recovered bodies were "buried deep in the ground and covered with waste," according to the OHCHR.
"Among the deceased were allegedly older people, women and wounded, while others were found tied with their hands...tied and stripped of their clothes," spokesperson Ravina Shamdasani said in a statement.
Palestinian Civil Defense spokesperson Mahmoud Basal said that some of the recovered bodies were hand-cuffed and clad in detainee uniforms. Basal accused the Israeli military of executing people and burying their bodies, the New York Times reported.
Volker Türk, the UN human rights chief, "expressed his horror" at both the mass graves and the destruction of Palestinian hospitals.
"Hospitals are entitled to very special protection under international humanitarian law. The intentional killing of civilians, detainees and others who are hors de combat [unable to participate in combat] is a war crime," Türk said.
In response to the UN's call for investigations, Israel released a statement claiming they exhumed bodies - but only so they could identify whether there were hostages buried among other bodies.
"The claim that the IDF buried Palestinian bodies is baseless and unfounded. During the IDF's operation in the area of Nasser Hospital, in accordance to the effort to locate hostages and missing persons, corpses buried by Palestinians in the area of Nasser hospital were examined," the statement read.
"The examination was carried out respectfully while maintaining the dignity of the deceased. Bodies examined, which did not belong to Israeli hostages, were returned to their place."
The Israeli statement made no mention of the other mass grave discovered near Al-Shifa Hospital.
At least one Palestinian alleges that Israeli forces took the bodies of two male relatives who were killed during Israel's offensive on Khan Younis.
"After I had buried them in an apartment, the [Israelis] came and moved their bodies," he told the BBC. "Every day we search for their bodies, but we fail to find them."