According to the statement, the IDF will unload the supplies and transfer the shipment to the Gaza Strip after it underwent an inspection to ensure that it did not include weaponry.
The Navy has held a number of drills in recent weeks to prepare for the arrival of the flotilla which is expected to try and break the Israel-imposed sea blockade on Gaza and dock in the newly-expanded port there.
The drills included the commandeering of the ships which could, military sources said Wednesday, include violent clashes depending on the response by the passengers on the vessels.
"We will do everything to ensure that the operation runs smoothly but are prepared for every possible scenario," one defense official explained.
On Wednesday evening, the IDF announced that it was planning to stop the flotilla of nine ships that are carrying hundreds of activists and thousands of tons of supplies. The IDF said that it planned to intercept the ships as they approached the Gaza Strip and urge them to turn around.
IDF: Shipment will be transferred to Gaza following inspection
"If they decide to continue sailing and do not listen to the instructions then they will be stopped, brought to Israel and treated by the Interior Ministry which will return them to the countries they came from," an IDF statement said.
Meanwhile Wednesday, the IDF continued its media blitz against the flotilla, organized by the Free Gaza organization, and released data claiming that all of the supplies the ships were carrying were already transferred by Israel to Gaza via land crossings on a regular basis.
"This flotilla is a provocation that is not needed considering the humanitarian situation in Gaza which is stable and good," said Col. Moshe Levi, commander of the IDF's Gaza Coordination and Liaison Administration. Levi said that 100 trucks, loaded with supplies, enter Gaza on a daily basis and that in the past two months over 1,200 tons of medical supplies were transferred to the ship.