Thirty activists, most of them Spanish, have met the ambassador, asking Madrid to put pressure on Greece to allow them to continue their mission, AFP reported.
They had then “decided to occupy the rooms,” one of the activists said.
The members of the flotilla say the Greek government is blocking the humanitarian flotilla on behalf of the Israeli regime.
Greece has so far barred three vessels from the Gaza Freedom Flotilla II from sailing for the besieged Palestinian territory.
Separately, American flotilla activists have staged a protest outside a courtroom where their captain faces charges for attempting to sail to Gaza without permission.
The US Audacity of Hope boat was prevented from leaving Greece on Friday and its captain, 60-year-old John Klusmire, was arrested.
Greece has recently expanded its relations with Israel, as the two sides are currently holding preliminary talks on potential energy deals.
The cash-strapped Greek government is also currently seeking additional sources of overseas investment, possibly from Israel, to offset its financial crisis.
The Tel Aviv regime has ordered the Israeli navy to use all possible means to prevent the incoming international aid flotilla from reaching the Gaza Strip, but the Gaza Freedom Flotilla II organizers insist that they will push ahead with their aid mission.