The latest bloodshed came just hours after the UN General Assembly called for an immediate ceasefire in the devastated territory.
Seven guards were killed in a strike in Rafah, while another attack left five guards dead in Khan Yunis, agency spokesman Mahmud Bassal said.
"The occupation once again targeted those securing the aid trucks," Bassal told AFP, adding that around 30 people, most of them children, were also wounded in the strikes.
"The trucks carrying flour were on their way to UNRWA warehouses," Bassal noted, referring to the United Nations agency for Palestinian refugees.
"The occupation aims to destroy all services for citizens across the Gaza Strip."
Witnesses later told AFP that residents looted flour from the trucks after the strikes.
The Israeli military said its forces "conducted precise strikes" overnight on armed Hamas militants present in the humanitarian corridor in southern Gaza.
"All of the terrorists that were eliminated were members of Hamas and planned to violently hijack humanitarian aid trucks and transfer them to Hamas in support of continuing terrorist activity, preventing them from reaching Gazan civilians, as was done in previous cases," the military alleged in a statement.
It insisted it "does not strike humanitarian aid trucks and the humanitarian corridor remains open and active".
The United Nations and other aid agencies have repeatedly warned about the acute humanitarian crisis in the Gaza Strip, exacerbated by the war that has persisted for more than 14 months.
'Apocalyptic'
"Conditions for people across the Gaza Strip are appalling and apocalyptic," UNRWA spokeswoman Louise Wateridge told journalists during a visit to Nuseirat in central Gaza.
She added that life-saving aid to "besieged areas in north Gaza governorate has been largely blocked" since the Israeli military launched a sweeping assault several weeks ago.
Israeli air strikes on two homes near Nuseirat refugee camp and Gaza City killed 21 more people, including children, the civil defence agency said.
Fifteen people, at least six of them children, died "as a result of an Israeli bombing" of a building sheltering displaced people near Nuseirat, Basal said.
The bodies of six others killed in a strike on an apartment in Gaza City were taken to a hospital morgue, he added.
In Khan Yunis, relatives gathered at the Nasser Hospital to mourn the dead and perform funeral rites.
Israel's offensive in Gaza has killed tens of thousands of people and devastated the coastal territory since a Hamas attack on southern Israel ignited the war.
In the latest diplomatic effort to end the violence, the UN General Assembly adopted a resolution on Wednesday calling for an immediate and unconditional ceasefire.
The non-binding resolution was rejected by the United States, Israel's main military backer.
However, in recent days, there have been indications that previously stalled ceasefire negotiations could be revived.
Families of the 96 hostages still in Gaza, including 34 the Israeli military says are dead, are pressing for their release.
Militants abducted 251 hostages during the October 7, 2023 attack on Israel, which killed 1,208 people, mostly civilians, according to an AFP tally based on official figures.
This count includes hostages who died or were killed while held in Gaza.
Israel's retaliatory offensive has killed at least 44,805 people in Gaza, a majority of them civilians, according to figures from the Hamas-run territory's health ministry that the United Nations considers reliable.
