“No greater threat exists to the security of Israel, to the entire region and, indeed, to the United States than a nuclear-armed Iran,” Panetta said in a speech to the American Israel Public Affairs Committee. “The Iranians now face a choice to either meet their international obligations and rejoin the community of nations or violate their international obligations and face the consequences.”

Beyond the forceful rhetoric, there was an element of fence-mending in Panetta’s remarks: In recent weeks, he and Joint Chiefs of Staff Chairman Gen. Martin Dempsey made several Iran-related comments that irritated Israel, prompted an unusual public rebuke from Republican senators and became campaign trail fodder for Republican presidential candidates.

The rift between the uniformed leadership and the Republican senators is unusual. Military commanders often team with Republican lawmakers to seek more resources and a more hawkish approach in Iraq and Afghanistan, sometimes over the objections of the Obama administration. On Iran, however, the generals seem wary of the GOP’s hawkishness and more in agreement with the White House’s measured approach.

Analysts interpreted Panetta’s and Dempsey’s earlier remarks as an effort to try to forestall a possible Israeli military strike aimed at Iran’s nuclear program — a strike that could complicate the U.S military’s already troubled efforts in Afghanistan and lead to retaliation against U.S. troops and sailors across the Middle East.

“The military is often cautious about commitments of military power,” former Rep. Lee Hamilton (D-Ind.) said in an interview. “They see the difficulty of this situation from a military standpoint, not only the attack itself but sustaining the attack over a period of days, if not weeks. … A very powerful factor here is what the Pentagon now calls persistent conflict or endless war. We have, in effect, been at war for 10 years, at least since 9/11.”

Hamilton, now director of the Center on Congress at Indiana University, said the “military is very worried about what they’re confronting with budget cuts and are just not anxious to take on another war.”

One of the leading hawks in the Iran debate, former Reagan and Bush administration official Elliott Abrams, said it isn’t surprising that the Pentagon is skittish about a new fight in the Middle East.

“They have to plan not for the most likely Iranian response but the worst possible Iranian response,” Abrams said. Still, he added, “if Iran’s response is to attack us in Afghanistan, it will be sorry and be sorry very soon. We have many ways of punishing Iran.”

Panetta landed in hot water early last month over Washington Post columnist David Ignatius’s report that Panetta believed Israel was likely to strike Iran by June and had “very directly” told the Israelis it would be a mistake to attack Iran now.

Dempsey ran into trouble a few weeks later in an interview with CNN’s Fareed Zakaria.

“We think that it’s not prudent at this point to decide to attack Iran. I mean, that’s been our counsel to our allies, the Israelis, well known, well documented,” Dempsey told Zakaria. “I’m confident that [the Israelis] understand our concerns, that a strike at this time would be destabilizing and wouldn’t achieve their long-term objectives.”

Dempsey also said he thought the Iranian government’s decisions were calculating enough to be influenced by outside pressure. “We are of the opinion that the Iranian regime is a rational actor,” he told CNN.

Israeli Prime Minister Benjamin Netanyahu complained to U.S. National Security Adviser Tom Donilon that Dempsey’s remarks, along with press reports that Israel saw as driven by the U.S. military, “only served the Iranians,” according to the Israeli newspaper Haaretz.

During a visit to Jerusalem last month, Senate Armed Services Committee members John McCain (R-Ariz.) and Lindsey Graham (R-S.C.) indicated they considered Dempsey’s remarks mistaken and unwise.

Iran “is continuing to pursue a nuclear weapons capability despite the growing consequences for this behavior: mounting international isolation, unprecedented sanctions that are increasingly cutting off the life blood of Iran’s economy and the very real threat of conflict,” McCain said. “It is hard to see this as rational behavior.”

McCain, the top Republican on the committee, also said the remarks suggested to the world that the U.S. and Israel were not in sync. “There should be no daylight between America and Israel in our assessment of the [Iranian] threat. … Unfortunately, there clearly is some,” McCain said.

“Gen. Dempsey is a fine man. But when he said that he thought the Iranians were rational actors, I just want to go on record. I don’t think it’s rational for a country to try to kill the Saudi Arabian ambassador in a restaurant in Washington. I don’t see what Iran is doing is being rational,” Graham told CNN.

The criticism of Dempsey continued this week with Republican presidential candidate Rick Santorum suggesting Dempsey is part of an effort to mislead Americans.

“The fact that we have the chairman of the Joint Chiefs saying we’re not sure yet that Iran is really going to pursue or has made the decision to develop a nuclear weapon just shows again the disconnect that they know we have, that the insincerity of our leaders in telling the truth to the American public about what is actually going on,” Santorum said during a speech Tuesday to AIPAC. “Rational actors don’t call for the destruction of other states or call them cancers.”

In his own speech to AIPAC, Mitt Romney didn’t mention Dempsey by name but said: “I do not believe that we should be issuing public warnings that create distance between the United States and Israel.”

Dempsey sought to calm the dustup by telling a Senate hearing last week that he simply had tried to discuss the timing of a possible Israeli strike.

“I didn’t counsel Israel not to attack. We’ve had a conversation with them about time, the issue of time,” the general said.

However, Dempsey stood by his comment on Iran’s rationality. “My view of this is we can’t afford to underestimate our potential adversaries by writing them off as irrational,” he said.

On Capitol Hill on Tuesday, another top U.S. general cautioned that military action would “just delay” Iran’s nuclear drive.

“I don’t see this going in the right direction until the full effect of the sanctions can accrue,” the head of Central Command, Gen. James Mattis, told the Senate Armed Services Committee. “Only the Iranian people can stop this program.”

There’s no indication that any of the remarks by Pentagon officials contradicted the advice the U.S. had been giving to Israel privately. However, they diverged from the public stance at that time of President Barack Obama, who insisted that the U.S. and Israel are “in lock step” on Iran.

Since then, Obama has moved closer to the Pentagon leaders’ remarks, making clear in speeches and interviews that he believes sanctions should be given time to work. The president has not embraced the “rational actor” formulation, and he has been careful to insist that he’s not trying to dictate how Israel should defend itself.

“It is deeply in everybody’s interests — the United States, Israel and the world’s — to see if this can be resolved in a peaceful fashion,” Obama said at a news conference Tuesday. “So this notion that somehow we have a choice to make in the next week or two weeks, or month or two months, is not borne out by the facts.”

Pentagon press secretary George Little told POLITICO, “The secretary’s public comments on these matters have been clear and consistent over time. He’s affirmed the U.S. commitment to the security of Israel and has also said that the Iranians cannot be allowed to have a nuclear weapon.”

In his speech to AIPAC, Panetta tried hard to win the audience’s trust, describing himself as a “lifelong friend of Israel” and recounting stories of saying Jewish prayers with Sen. Chuck Schumer (D-N.Y.) when they shared a Washington home. Panetta, who met with Netanyahu on Monday, also went out of his way to describe his chumminess with Israeli officials.

“I can tell you, after our operation to get [Osama] bin Laden, the first congratulations I got were from my buddies in Mossad,” Panetta said.

He emphasized his close relationship with Israeli Defense Minister Ehud Barak even as he acknowledged some disagreements. “There is no minister of defense that I have met with more regularly or consulted more often,” Panetta said. “We talk. We argue. We eat. We are family,” he said to laughter from the crowd.