The cargo ship Hope will depart from Lavrio, some 60 kilometres (37 miles) southeast of Athens, the Libyan embassy said.
"This is a humanitarian mission expected to sail later on Friday," an embassy official told AFP.
The Tripoli-based Gaddafi International Charity and Development Association said it was sending a cargo ship "loaded with about 2,000 tons of humanitarian aid in the form of foodstuff and medications".
The ship will also carry "a number of supporters who are keen on expressing solidarity with the Palestinian people in the plight amidst the siege imposed on Gaza," the organisation added in a faxed statement.
The charity is chaired by Saif Al-Islam Gaddafi, second son of the Libyan leader.
Eight Turks and a dual US-Turkish citizen were killed in May when Israeli commandos attacked a flotilla heading for Gaza, sparking a furious row with Ankara which wants Israel to apologise or accept an international probe.
Source: AFP Global Edition