After a visit to the crossing, the Gaza chief of the UN agency for Palestinian refugees (UNRWA), John Ging, said the 'partial reopening' did little to ease Palestinian hardships.
Ging said the crossing was only operating at 10% of its capacity and called on all involved to open it up fully.
"At 10% we are not even meeting today's needs", he said.
"I sincerely hope that today's opening of Karni is the beginning of a return to normality; for Gazans, this is the first rationing of bread in living memory," Ging said.
UNRWA has also run out of fuel in Gaza.
"We are operating with what is left in the tanks of our cars," Ging said.
"Once we get the food in, we will need fuel to distribute it," he said.
A Palestinian security official said on Tuesday that cargo trucks were beginning to move into the Palestinian territory via the al-Mintar or Karni crossing. Israel's defence ministry declined to say for how long it would remain open.
On Monday the crossing, which has been closed for most of the year, was partially reopened for less than an hour to goods leaving Israel destined for the Gaza Strip.
A Palestinian security official later said the Israelis had ordered the central Gaza checkpoint to close again because of an "attack alert".
Before the crossing was opened on Tuesday, an official from the Israeli prime minister's office said: "We will reopen Karni on a temporary basis to dozens of trucks carrying foodstuffs, particularly flour, but we will close it immediately in case of threat of a terrorist attack."
The UNRWA had said on Sunday that residents of the territory were running short of staple foods.
"The crossing point must be open for a sustainable amount of time to recover the stocks," the agency had stressed.
Israeli public radio estimated that about 90 trucks of flour, oil and rice would be allowed to cross if the checkpoint stayed open for the entire day.
An Israeli official denied that any US pressure had been brought to bear for the reopening.
On Sunday, the US ambassador in Tel Aviv hosted talks at which the Palestinians pressed for al-Mintar to reopen.