Border officials had held up a six-member delegation returning from truce talks in Cairo after insisting on searching their bags, AFP reported.
The officials allowed five members to cross, but prevented Gaza-based Hamas spokesman Ayman Taha, who was carrying the cash, from entering Gaza with the money.
He was allowed back into Gaza late Thursday after Egyptian authorities insisted he put the money in a bank in the north Sinai town of Arish, al-Arabiya news channel reported.
Asked by al-Arabiya about the source of the money, Taha said: "This is not the question we should ask. We should rather ask how much longer we will be carrying money in bags."
Gaza has a severe shortage of cash caused by the Israeli blockade and other sanctions by the Egyptian regime.
"I was just carrying the money for the Palestinian people who suffered from the war and the siege," Taha said.
Israel's air and ground offensive in the Gaza Strip has destroyed the tiny enclave's infrastructure and killed 1,330 Palestinians. 5,450 more were injured while 14,000 homes and 68 government buildings were damaged.
On Thursday, Israel gave a go-ahead for a cash delivery into the Gaza Strip for the first time since its recent military offensive against Gaza, Israeli media reports said.
The reports said USD 42m would be transferred from the West Bank to banks in the Gaza Strip in order to pay around 70,000 employees of the Palestinian Authority of President Mahmoud Abbas.
In December 2006, Hamas Prime Minister Ismail Haniya was forced to leave USD 35m on the Egyptian side of Rafah. The money was then transferred to a Palestinian Authority account of Mahmoud Abbas.
In another development, Egypt closed the Rafah crossing to all but what it called exceptional cases on Thursday.
"No humanitarian, media or medical delegations will be allowed through, nor will medical aid deliveries be permitted," an Egyptian border official had told AFP.
Egypt refuses to permanently open the crossing in the absence of EU monitors and representatives of Palestinian president Mahmoud Abbas.
Egyptian President Hosni Mubarak who has been in office for 28 years, has blamed Hamas for the massacre of hundreds of Palestinians in the Gaza war, saying the democratically-elected rulers of the coastal territory must be held responsible for the Israeli operations.