Ahmed Abul Gheit, Egypt's foreign minister, said in remarks published on Saturday that members of Viva Palestina, the last convoy allowed through, had "committed hostile acts, even criminal ones" on Egyptian soil.
"Egypt will no longer allow convoys, regardless of their origin or who is organising them, from crossing its territory," he told government-backed newspaper Al-Ahram.
More than 50 people were wounded during a clash between Egyptian authorities and international members of the convoy on Tuesday after Egypt decided to allow 139 vehicles to enter Gaza, but said a remaining 59 vehicles would have to pass via Israel.
The Rafah border is the only crossing point into the Palestinian territory not controlled by Israel.However, both Rafah and the Israeli-controlled crossings have largely remained sealed since 2007, when the Palestinian group Hamas gained control of the Strip.
George Galloway, the British MP leading Viva Palestina, was himself deported by the Egyptian government on Friday.The politician was picked up by Egyptian officials at Rafah and driven to Cairo, the capital, where he was placed on a flight back to London.
The Egyptian foreign ministry said Galloway had been declared "persona non grata" and would not be allowed to return to the country, accusing him of incitement over his criticism of the government.
Arrest warrants were also issued for seven other members of the convoy after being accused of inciting riots in El-Arish, the Mediterranean port town where Viva Palestina entered the country.
The Respect Party MP has been vocal in his criticism of Egyptian authorities in recent days.
"It's always been a badge of honour to be deported by a tin-pot dictator and that's what happened," he said after arriving at London's Heathrow airport.
Abul Gheit, who spoke to Al-Ahram during a visit to Washington, said future aid convoys will have to turn their supplies over to El-Arish's Red Crescent chapter.
The relief organisation would then be responsible for transferring the aid to its Palestinian counterpart.
Israel and Egypt have severely restricted travel to and from the Gaza Strip, and only very basic supplies are allowed in.
Aid organisations say the siege has placed Gazans in a dire situation, made worse by the Israel's offensive last year that reduced much of the territory to ruins.