Ten lorries carrying flour and rice were taken from the Palestinian side of the Kerem Shalom crossing, the UN's Relief and Works Agency (Unrwa) said.
Hamas admitted a "mistake" had been made and says it will return the goods.
But Unrwa says deliveries will not restart until it has assurances that such seizures will not happen again.
UN Secretary General Ban Ki-moon said Hamas must immediately release the seized aid shipments.
He also called on Hamas "to refrain from interference with the provision and distribution of humanitarian assistance in Gaza".
Gaza is facing a humanitarian crisis after Israel's recent three-week offensive.
About half the population is dependent on UN food aid.
Israel intensified a blockade on the territory 19 months ago when Hamas took over the territory.
The lifting of the blockade is among Hamas' demands for agreeing a long-term truce with Israel.
On Friday, the group's exiled leader, Khaled Meshaal, told a rally in Syria that Israel still had not given the necessary undertakings for such a truce.
Second incident
Unrwa said the food had been imported from Egypt, and had been due to be collected by its staff at the Kerem Shalom crossing in southern Gaza on Friday.
The UN had recently increased its food distribution to Gazans
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"The food was taken away by trucks contracted by the ministry of social affairs," the agency said in a statement.
It said aid deliveries would only be resumed if Hamas returned all the aid and provided "credible assurances" that it would not happen again.
It was the second incident in three days. On Tuesday, 3,500 blankets and more than 400 food parcels were seized at gunpoint from a distribution centre in Gaza, the UN said.
The Hamas government's social affairs minister, Ahmed al Kurd, ordered "the aid to be returned to the agency if it turns out it is indeed its property", Hamas spokesman Fawzi Barhum said, according to AFP news agency.
UN-Hamas tensions
Earlier in the week, Mr Kurd warned Unrwa not to "become a political player in Gaza". He said all aid should be distributed through Hamas.
But Hamas's rapid attempt to rectify the situation - at least once Unrwa announced its suspension of imports publicly - suggests it does understand how crucial the UN's aid work is, our correspondent says.