"Israel is a sovereign nation and every sovereign nation has the right to defend itself and protect itself. Israel will do that. It must do that," Hagel told reporters aboard a U.S. military flight to Israel.
"Iran presents a threat in its nuclear program," Hagel said. "Israel will make the decisions that Israel must make to protect itself and defend itself."
Iran insists its nuclear program is peaceful and denies trying to build nuclear weapons.
"Military options, I think most of us feel, should be the last option," Hagel said. "If that is an option that's required, then we'll have to make that decision.
"But I think it's our sense -- the United States and many of our allies -- that these other tracks do have some time to continue to try to influence the outcome in Iran," Hagel said.
Hagel acknowledged Sunday there "may well be some differences" between Washington and Jerusalem on the timeline in which Iran might develop nuclear weapons.
But he said there was "no daylight there at all" between the two countries on the goal of preventing Iran "from acquiring that nuclear capacity."
A senior defense official traveling with Hagel told The Wall Street Journal Washington remained "concerned about the unintended consequences of a prospective Israeli strike on Iran" and said Hagel was "very aware" of those concerns.
During a two-day visit, Hagel was to meet with Israeli Prime Minister Binyamin Netanyahu and new Defense Minister Moshe Yaalon for talks about threats posed by Iran's nuclear program and about Syria's civil war.
He also was to meet with Israeli President Shimon Peres to discuss military issues and ways of advancing the Israeli-Palestinian peace process.
Hagel had dinner with Yaalon Sunday night after visiting Jerusalem's Yad Vashem Holocaust memorial museum.
Hagel told reporters as he flew to Israel he intended to offer to sell Israel new, advanced weapons that could make an attack on Iran more decisive.
These include V-22 Osprey tilt-rotor aircraft, which can transport troops and patrol borders and nearby seas, and KC-135 Stratotanker aerial refueling military aircraft, as well as anti-radiation missiles and advanced radar for Israeli fighters.
The Pentagon said Friday it was finalizing the deal.
The KC-135s could be especially useful in the event of an Israeli strike on Iran because the tankers would let Israeli warplanes travel longer distances than they could earlier, the Journal said.
Experts have long said Israel's lack of ample refueling capacity was a key obstacle to an effective Israeli strike on Iran.
Washington has not offered to sell Jerusalem the 30,000-pound Massive Ordinance Penetrator, the biggest "bunker buster" bomb the U.S. Air Force has, U.S. and Israeli officials told the Journal.
The bomb is designed specifically to take out hardened targets and targets buried deep underground -- like what the West says Iran built to protect its nuclear program from an Israeli strike.
Hagel said the prospective weapons sales served as "another very clear signal to Iran" a military option was really on the table.
The sales to Israel are expected to be part of a broader preliminary $10 billion package that also would provide more advanced air-to-ground missiles to U.S. Persian Gulf allies Saudi Arabia and the United Arab Emirates.
The UAE will be allowed to purchase some two dozen F-16 Fighting Falcon warplanes, and both Saudi Arabia and the emirates will be allowed to buy precision air-to-ground missiles.
Hagel also plans to visit Saudi Arabia and the UAE this week, as well as Jordan and Egypt.
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