The incident occurred days after the Israeli navy seized a Norwegian-flagged boat belonging to the flotilla.
The vessel - Freedom for Gaza - was sailing under the Swedish flag and was carrying 12 people. It was taken to the Israeli port of Ashdod on Saturday, the Israeli military said, adding the people on board were taken for "further inquiry".
"The ship was monitored and was intercepted in accordance with international law," the military said in a statement. "The [military] clarified to the ship's passengers that they are violating the legal naval blockade and that any humanitarian merchandise can be transferred to Gaza through the Port of Ashdod," the statement added.
The Norwegian-flagged vessel, named al-Awda (Return), was seized some 60 nautical miles off the coast in international waters last Sunday.
Torstein Dahle, the head of Ship to Gaza Norway, which had organized the trip was later quoted by media as saying that Israeli security forces had struck the captain of the Ship on the head before ordering him to sail to the coastline of the Israeli-occupied territories instead.
Oslo has demanded that Tel Aviv explain the legal grounds on which it seized the vessel and its passengers. The boat was carrying 22 people, including two Israelis, who were immediately released after the boat was captured.
The first "Freedom Flotilla", carrying medical equipment for Gaza, was intercepted last month.
Four boats left from Scandinavia in mid-May and stopped in some 28 ports along the way, with two remaining behind after a recent stop in the Italian port of Palermo.
Israel has enforced the blockade under the excuse of preventing arms smuggling into Gaza for the Palestinian resistance movement of Hamas.
Under the blockade, Gaza, which hosts some two million Palestinians, has already seen an unfolding economic and humanitarian crisis. The United Nations has warned that the overall conditions in the enclave could make it “uninhabitable” by 2020.
