The military said the cargo vessel "Victoria" initially departed from the Lattakia port in Syria before proceeding to the Mercin port in Turkey. From there it departed for the port of Alexandria in Egypt. Israel says that Turkey had no involvement in the arms shipment.
Israel's military spokesman, Brig. Gen. Avi Benayahu, said at least three crates of weapons were uncovered on board. Hundreds of others will be inspected once the ship arrives in Israel.
Benayahu said Syria's fingerprints were all over the shipment.
"Apparently we'll find more evidence of the Iran, Syria, Hezbollah axis," he told Israel's Army radio.
Israel has long blamed Iran and Syria for smuggling weapons to militants in Gaza and Lebanon, a claim both nations have denied. Iran and Syria are the main backers for two of Israel's main foes - Hezbollah guerrillas in Lebanon and Hamas militants in Gaza.
The Victoria is German-owned, operated by a French shipping company and was sailing under a Liberian flag, the military said.
The interception occurred about 200 miles (320 kilometers) off Israel's Mediterranean coast and Israeli troops met no resistance. The vessel was being hauled back to the Israeli port of Ashdod, according to the military.
It said the discovery was made during a routine navy activity to prevent arms smuggling.
The military gave no details on what types of arms were on board, but said it was intended for the use of militant organizations operating in the Gaza Strip. Israel says that Hamas routinely has arms shipments delivered to Egypt, and then smuggled into neighboring Gaza through a network of tunnels.
German, French and Liberian authorities were notified of the seizure.
The operation was reminiscent of the November 2009 Israeli takeover of the Iranian Francop vessel off the coast of Cyprus. Israel captured hundreds of tons of rockets, missiles, mortars, grenades and anti-tank weapons on board headed to Hezbollah guerrillas in Lebanon.
In May 2001 off its coast, Israel captured the vessel Santorini, packed with explosives that Israel said were sent from Hezbollah to Palestinian militant groups.
In January 2002, Israeli forces stormed the Karine A freighter on the Red Sea, and confiscated what the military said was 50 tons of missiles, mortars, rifles and ammunition headed for Palestinian militants in the Gaza Strip.
"Terror from the sea is something that we know well and we are trying to battle with," said Lt. Col. Avital Leibovitch, a military spokeswoman.
Israel's announcement that Turkey was not involved in the arms shipment appeared to be an effort to diffuse any potential tensions with its former Mideast ally.
Last May, Israeli commandoes raided a Turkish ship trying to break a naval blockade of Gaza and killed nine pro-Palestinian activists on board.