UNRWA said 10 truckloads of rice and flour, more than 200 tonnes, were seized last night on the Palestinian side of the Kerem Shalom crossing with Israel.
However Hamas has indicated the goods will be returned, saying the incident was a mistake.
'UNRWA has suspended all imports of aid into the Gaza Strip following the confiscation of hundreds of tonnes of food aid,' the UN agency for Palestinian refugees said.
Hamas promptly said the aid would be returned, blaming the incident on confusion at the Kerem Shalom crossing.
Hamas social affairs minister Ahmed al-Kurd ordered 'the aid to be returned to the agency if it turns out it is indeed its property'.
'The aid supplies were loaded onto trucks by mistake as no government representative was present. The drivers did not know which supplies were UNRWA's and which were the government's,' he said.
'UNRWA's suspension of imports will remain in effect until the aid is returned and the agency is given credible assurances from the Hamas government in Gaza that there will be no repeat of these thefts,' the UNRWA statement said.
UNRWA spokesman Chris Gunness told AFP 'the people of Gaza have suffered quite enough, and anything that puts in jeopardy the international system is extremely dangerous.'
The incident is the second of its kind in three days. On Tuesday, 3,500 blankets and more than 400 food parcels were seized at gunpoint from a distribution store in a Gaza City refugee camp.
The deliveries are an exception to the crippling Israeli blockade of Gaza, but Israel has regularly responded to Palestinian militant rocket attacks by preventing aid convoys from entering the besieged territory.
UNRWA plays a key role in distributing aid in the impoverished enclave and says it is handing out food assistance to 900,000 out of the 1.5-million population.
