The centres were closed on Saturday because the GHF said the Palestinian Islamist militia Hamas was threatening it.
One of the centres in Rafah, in southern Gaza, would reopen at noon on Sunday (7pm AEST), the GHF said in a statement on its Arabic-language Facebook page.
At the same time, residents were told not to approach the centre before opening hours. Otherwise, the GHF may not be able to distribute food packages, it said.
The GHF also closed its distribution centres on Friday for safety reasons and urged residents to stay away from the facilities.
Around two weeks ago, Israel eased its blockade of aid deliveries to Gaza. The distribution of aid was taken over by the GHF, bypassing UN aid organisations and other initiatives.
The organisation has faced criticism for bypassing established aid networks, as well as for allegedly endangering civilians and breaching widely accepted standards of impartial humanitarian assistance.
Last week, the UN said increasing numbers of Palestinians were "vulnerable to starvation", with daily energy intake well below what a human body needs to survive.
Meanwhile, Palestinian medical sources said at least 60 people had been killed in the Gaza Strip since early Saturday.
Dozens more have been injured, the Hamas-controlled Health Ministry said. The Israeli army initially provided no information, and the figures could not be independently verified.
The death toll is rising by the hour as the Israeli military continues to attack various locations in the sealed-off territory.
The Palestinian news agency WAFA reported deaths in the areas around Khan Younis and Rafah in the south of the embattled strip, as well as in Gaza City further north. There was no initial comment from the Israeli military.
Israel has been fighting Hamas in the Gaza Strip since the militia and its allies launched an unprecedented attack on Israel on October 7, 2023, killing some 1200 people and abducting 250.
The subsequent war has killed more than 54,000 people in Gaza, according to the Hamas-controlled health ministry. The figures do not distinguish between civilian and military deaths.
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