The Israeli navy boarded the Gaza-bound "Estelle" ship, which was seeking to breach Israel's naval blockade on Gaza, the IDF confirmed at 11:40 am on Saturday.
The army said the soldiers seized control of the ship, which is carrying pro-Palestinian activists.
"When the passengers made it clear that they would not cooperate or accept the invitation to sail to the Ashdod Port, it was decided to seize the vessel and bring it to the Ashdod Port," the army said in a statement.
"The Navy force operated as planned to guarantee the safety of the soldiers and passengers on the deck. The soldiers did not use force while seizing the ship."
The army added that once the ship reaches Ashdod the passengers will be handed over to police and immigration authorities.
The IDF spokesperson added that any organization or country wishing to reach Gaza or move humanitarian aid is able to do so legally and orderly at all times through land passages and in coordination with the Israeli authorities.