Legal problems facing the flotilla organizers included severe difficulties in securing insurance for the boats due to major insurers having been approached by the NGO Shurat HaDin (Israel Law Center), which also filed a complaint with the Greek coast guard regarding the suspected lack of seaworthiness of seven of the boats comprising the flotilla. In addition, Shurat HaDin approached the maritime communications company Inmarsat, warning of the potential for damages suits and charges of aiding and abetting terrorism should it provide satellite services to the Gaza-bound ships. The NGO also filed lawsuits against the flotilla on behalf of U.S. citizens.

Public exposure of the connections of some of the flotilla’s organizers to Hamas also caused significant problems for its organizers. Just Journalism detailed the alleged Hamas connections of the European Campaign to End the Siege on Gaza official Mohammed Sawalha, and four Dutch journalists pulled out of the flotilla after having discovered the extent of involvement of the Hamas-linked activist Amin Abou Rashed in the organization of the Dutch-Italian boat. The journalists also complained of lack of transparency on the part of the flotilla organizers.

The internal economic and political crisis situation in Greece, where most of the flotilla’s boats had grouped, brought about a general strike which contributed to the delay in the flotilla’s departure as ports and marinas closed down as a result. In addition, a possible case of sabotage to the propeller of the Swedish-Norwegian boat in Greece and a similar (though disputed) incident concerning the Irish boat in Turkey incurred heavy expense for repairs and necessitated further postponement of departure.