Some 520 activists broke down the gate at the port in al-Arish late on Tuesday in protest against an Egyptian decision to ship some of the goods through Israel, medical workers and protesters said.
The protests were sparked by an Egyptian decision to allow 139 vehicles to enter Gaza through the Rafah crossing, about 45km from the port in al-Arish, but requiring a remaining 59 vehicles to pass via Israel.
Around 40 members of the convoy had minor injuries while over a dozen policemen were hurt in the clashes with protesters, who also blocked the two entrances to the Sinai port with vehicles, medical workers said.
The Viva Palestina convoy, led by George Galloway, the British MP, had already been delayed by more than a week, after he and a delegation of Turkish MPs failed to persuade the Egyptians to change their mind.
The convoy of nearly 200 vehicles arrived in al-Arish on Monday after a dispute with Cairo on the route.
But the arrival came after a bitter dispute between its organisers and the government, which banned the convoy from entering Egypt's Sinai from Jordan by ferry, forcing it to drive north to the Syrian port of Lattakia.
The convoy with 210 lorries full of medicine and other supplies set out from the UK nearly a month ago.
Israel and Egypt have severely restricted travel to and from the Gaza Strip since Hamas seized power there in June 2007, after winning Palestinian legislative elections in 2006.
The blockade currrently allows only very basic supplies into Gaza.
The siege has severely restricted essential supplies and placed Gazans in a dire situation, made worse by Israel's military assault last winter that reduced much of the territory to ruins.
Hamas has accused Egypt of reinforcing the siege imposed.
Fawzi Barhoum, a spokesman for the group, told Al Jazeera on Wednesday that Egypt's moves to ban the Gaza aid convoy from reaching the enclave and to build an underground steel wall are deliberate policies that reinforce its participation in the siege.
He said that such practices are unjustifiable and frustrating for Palestinian expectations from the Egyptian side.
In other Gaza-related news, a Palestinian fighter was reportedly killed and four others wounded in an Israeli air attack on Tuesday in the city of Khan Younis, according to a security source.
An Israeli military spokeswoman said Israel had launched the raid against fighters "planning to fire rockets at southern Israel".
The armed wing of a group called the Popular Resistance Committee said its members had been targeted by the attack.