The Israeli military said it had fired warning shots at suspects who approached its troops after they did not heed calls to stop, about a kilometre away from an aid distribution site that was not active at the time.
Gaza Strip resident Mohammed al-Khalidi said he was in the group approaching the site and heard no warnings before the firing began.
"We thought they came out to organise us so we can get aid, suddenly (I) saw the jeeps coming from one side, and the tanks from the other and started shooting at us," he said.
The Gaza Humanitarian Foundation, a US-backed group which runs the aid site, said there were no incidents or fatalities there on Saturday and that it has repeatedly warned people not to travel to its distribution points in the dark.
"The reported IDF (Israel Defence Forces) activity resulting in fatalities occurred hours before our sites opened and our understanding is most of the casualties occurred several kilometres away from the nearest GHF site," it said.
The Israeli military said it was reviewing the incident.
GHF uses private US security and logistics companies to get supplies into the Gaza Strip, largely bypassing a United Nations-led system that Israel alleges has let Hamas-led militants loot aid shipments intended for civilians.
Hamas denies the accusation.
The UN has called the GHF's model unsafe and a breach of humanitarian impartiality standards, which GHF denies.
On Tuesday, the UN rights office in Geneva said it had recorded at least 875 killings within the past six weeks in the vicinity of aid sites and food convoys in the Gaza Strip - the majority of them close to GHF distribution points.
Most of those deaths were caused by gunfire that locals have blamed on the Israeli military.
The military has acknowledged that civilians were harmed, saying that Israeli forces had been issued new instructions with "lessons learned".
At least 50 more people were killed in other Israeli attacks across the enclave on Saturday, health officials said, including one strike that killed the head of the Hamas-run police force in Nuseirat in the centre of the Gaza Strip and 11 of his family members.
The Israeli military said that it had struck militants' weapon depots and sniping posts in a few locations in the enclave.
The war began when Hamas-led militants stormed into Israel on October 7, 2023, killing 1200 people, mostly civilians and taking 251 hostages back to the Gaza Strip.
The Israeli military campaign against Hamas in the strip has since killed about 58,000 Palestinians, most of them civilians according to health officials, displaced almost the entire population and plunged the enclave into a humanitarian crisis, leaving much of the territory in ruins.
Israel and Hamas are engaged in indirect talks in Doha aimed at reaching a US-proposed 60-day ceasefire and a hostage deal mediated by Egypt and Qatar, although there has been no sign of any imminent breakthrough.
At least 20 of the remaining 50 hostages are believed to still be alive.
Einav Zangauker, whose son Matan was kidnapped from his kibbutz home and is held by Hamas, urged Israel's leaders to make a deal with the militant group.
"An entire people wants to bring all 50 hostages home and end the war," Zangauker said in a statement outside Israel's defence headquarters in Tel Aviv.
"My Matan is alone in the tunnels," she said, "He has no more time".
