The ship, known as Victoria, was flying a Liberian flag, and was seized by the navy in the Mediterranean Sea, 200 miles off of Israel's coast.
The Victoria was boarded by commandos from the Israeli Navy's Flotilla 13, also known as the Shayetet, arrived in the Ashdod port on Tuesday evening.
An initial inspection of the cargo revealed the ship was carrying weapons. The exact amount is to be determined.
The crew, questioned by the Navy Commando, was not aware that the cargo contained weaponry.
The ship set sail Monday night from the port of Lattakai in Syria and from there it traveled to Turkey. There, it was supposed to unload the weapons, which would travel by land to Gaza. The IDF's assessment is that the weapons did not originate in Turkey, but that the containers were unloaded there and transferred onto the Victoria.
The port of Lattakai is the same port where two Iranian war ships docked in February on their way to the Suez Canal. At the time, IDF officials raised concerns of the possibility that they were carrying weapons intended for terrorists organizations, but there was no confirmation.
"The operation was approved as necessary in accordance with government directives in light of Chief of the General Staff Lt. Gen. Benny Gantz's recommendations," an IDF statement read.
Gantz updated Defense Minister Ehud Barak about the findings on-board the vessel earlier in the morning.
"The IDF and the Ministry of Foreign Affairs alerted German authorities about the interception of the "Victoria" due to the German ownership of the ship," the statement said.
In addition, the government of Liberia, whose flag it was flying under, was notified, as well as France, due to the French shipping company.
The Israeli Navy has conducted numerous operations over the years against Iranian smuggling to Hamas and Hezbollah.
Foreign reports attribute bombings of truck convoys in Sudan as well as arms ships in the Red Sea in recent years to the IDF.
In November 2009, the Israeli Navy seized the Francop cargo ship, which was carrying 500 tons of weaponry from Iran to Hezbollah in Lebanon, including Katyusha rockets and grenades. At the time, IDF officers said the amount was enough to sustain Hezbollah for several weeks of war.