Yousseuf Sawani, executive director of the Gaddafi Foundation which chartered the vessel, said that eight Israeli warships had surrounded the Libyan aid ship, preventing it from continuing its journey to Gaza.
"It was unacceptable for us to enter into a confrontation and risk bloodshed," Sawani said.
"The aims of Amalthea have been achieved without bloodshed and the result is gains for the Palestinians."
The charity is headed by the son of Muammar Gaddafi, the Libyan leader, and carried supporters who were "keen on expressing solidarity with the Palestinian people in the plight amidst the siege imposed on Gaza".
A separate attempt by Jordanian activists and trade unionists to deliver aid and medical supplies to Gaza was blocked on Thursday by Egyptian authorities - the second incident in less than a month.
A convoy of 150 people, including "unionists, journalists and academics", travelled overland in 25 vehicles from Jordan to the Egyptian Rafah crossing.
"We are shocked that Egypt prevents us from delivering aid and medical supplies to Gaza"
Ahmad Armuti, president of the Jordanian trade unions' council
"We are shocked that Egypt prevents us from delivering aid and medical supplies to Gaza," Ahmad Armuti, president of a trade unions' council, said.
"We regret, reject and condemn Egypt's unacceptable position, not only towards our brave people of Gaza, but also towards all Jordanians."
Armuti called on the Jordanian government to demand clarification from Egypt, which "should be pressed to change its position".
"This will not stop the Jordanian trade unions from working hard to break the unjust blockade and resisting any form of normalisation with the Zionist entity," he said.
Late last month, Egypt banned several Jordanian trade unionists from Gaza through Rafah, Gaza's only crossing to bypass Israel, saying they had failed to give prior notice of their arrival.
Egypt had kept Rafah largely closed since Hamas took control of Gaza in 2007, but Hosni Mubarak, the Egyptian president, ordered it open after a deadly Israeli naval raid on a Gaza-bound aid flotilla on May 31.
Nine pro-Palestinian activists - eight Turks and a dual US-Turkish citizen - were killed after Israeli soldiers boarded the lead ship Mavi Marmara.
Following an international outcry over the raid, Israel eased restrictions on the Gaza Strip, allowing some previously banned items into the territory.
But construction materials remain heavily restricted, Gazans have very limited freedom of movement, and Israel still enforces a naval blockade on the territory.