TZEELIM, Israel—While the U.S. and Israeli diplomatic relations weather their choppiest phase in years, behind the scenes, military commanders from the two countries have dramatically stepped up cooperation.

The intensified partnership is part of the Obama administration's broader policy of boosting military support for American allies in the Mideast amid heightened tensions with Iran and its allies such as Hezbollah and Hamas, according to U.S. officials. The Obama administration believes it may also help induce Israeli Prime Minister Benjamin Netanyahu to make concessions in talks with Palestinians, these officials said.

Marines joined Israeli soldiers for an infantry exercise in the Negev desert this month, in what officials call the largest-ever joint U.S.-Israeli drill. Charles Levinson / The Wall Street Journal

With improved security in the area since the second Intifada, Israel removes a security barrier around the West Bank settlement town of Gilo. Video Courtesy of Reuters.

U.S. military aid to Israel has increased markedly this year. Top-ranking U.S. and Israeli soldiers have shuttled between Tel Aviv and Washington with unusual frequency in recent months. A series of joint military exercises in Israel over the past monthshas included a record number of American troops.

This month, about 200 U.S. Marines joined a battalion of Israeli soldiers for an all-night march through the Negev desert, the culmination of three weeks of joint drills. As dawn approached, they crept up on a mock village, an Israeli military-built recreation of a typical Palestinian hamlet, used for combat training.

Explosions, triggered by pyrotechnics engineers, shook the night. Soldiers from another Israeli unit, playing the role of Arab guerrillas, crouched in the fake village's narrow allies and empty cinderblock homes. They shouted "Allahu Akbar," Arabic for "God is Great," and rattled off rounds of blank ammunition from machine guns at the invading U.S. and Israeli forces.

Behind a dune on the village's edge, a U.S. Marine company commander conferred with his Israeli counterpart before the two barked orders—the Marine in English, the Israeli in Hebrew—to soldiers scattered behind them. As dawn gave way to the Negev desert's grinding August heat, the forces battled house-to-house in mock battle, as Israeli and Marine generals watched on from the sidelines.

The exercise was the biggest U.S.-Israeli joint infantry exercise ever, according to officials. By comparison, at the same exercise last year, there were only around 20 U.S. Marines involved. In the fall, there will be an even bigger joint infantry exercise involving tanks and armored vehicles, officials said.

In October, a missile-defense exercise between the U.S. and Israeli militaries, brought in more than 1,000 U.S. soldiers, making it the single biggest U.S.-Israeli joint military exercise in the two nations' histories.

Two joint U.S.-Israel committees, the U.S.-Israel Joint Political Military Group and the Defense Policy Advisory Group, which were established years ago and had fallen into disuse, have been beefed up with senior officials, including Undersecretary of Defense for Policy, Michele Flournoy, the top-ranking civilian at the Pentagon, Israeli and U.S. officials said.

The military cooperation began to intensify even as diplomatic relations between Washington and Israel frayed. The effort stems from policy directives the White House gave the Pentagon early in Mr. Obama's presidency to "deepen and expand the quantity and intensity of cooperation to the fullest extent," according to a senior administration official.

Officials in Washington and Israel continue to say they haven't ruled out a military strike against Iran amid Tehran's nuclear standoff with the West. But the new cooperation appears to be part saber-rattling at Iran and part reassuring Israel that the U.S. is fully committed to its security.

The senior U.S. official said President Barack Obama felt the increased military support is necessary to assure Israel's security against mounting regional threats, including Iran and its allies: Syria, the Gaza-based Hamas and Hezbollah in Lebanon. "History has shown that Israel is more willing to take risks for peace when it feels it is capable of addressing its security needs," the official said.

U.S. military aid to Israel reached a high of $2.78 billion in 2010, up from $2.55 billion in 2009. It is slated to jump to $3 billion in 2011. The Obama administration has also requested an additional $205 million to fund a short-range rocket defense shield known as Iron Dome.

Washington's stepped-up military support comes amid similar moves to strengthen military ties with America's Arab allies in the region, including those that don't maintain ties with Israel.

This week, the Obama administration said it intended to provide new Patriot missile batteries to Kuwait. And Washington is readying a $60 billion sale of advanced F-15 fighter jets and attack helicopters to Saudi Arabia.

Some outside observers say there may be an ulterior motive for the increased cooperation: To better keep tabs on Israel at a time when many in Washington are concerned that Israel could launch a military strike, unilaterally and without warning, against Iran's nuclear facilities.

"We want to keep Israel in the box militarily, and a strong personal and organizational relationship gives us leverage," said Jeff White, who spent 34 years with the Defense Intelligence Agency, before joining the Washington Institute for Near East Policy, a think tank.

The senior administration official said the relationship isn't a means for the U.S. to keep Israel in check, but rather about sharing intelligence and consulting on strategy, for instance vis-à-vis Iran. He said that due to the closeness of the relationship, the administration believes there is no chance of misunderstandings or surprises by Israel.

The Obama and Netanyahu administrations clashed soon after both leaders took power, amid different approaches to dealing with the Palestinians and the Mideast peace process. Washington has tried to mend the rift, recently extending a warm reception to Mr. Netanyahu at the White House.

U.S. and Israeli officials both say the improved military coordination began even as political relations between the two countries were nose diving. But the administration appears now to be showcasing the military support more as part of its efforts to patch over past differences.

Many details surrounding the U.S.-Israeli military cooperation remain classified, but some have emerged publicly. In the past year, record numbers of soldiers from both countries have participated in joint drills. In the exercises, the two militaries have been drilling as a coalition force, battling a common enemy for the first time, just as the U.S. does with its North Atlantic Treaty Organization allies, according to U.S. and Israeli commanders.

Meanwhile, visits by the Israeli and American military brass have jumped dramatically. Since becoming Chairman of the Joint Chiefs of Staff in 2007, Adm. Michael Mullen has made four visits to Israel, two of them this year alone. Before Adm. Mullen, no chairman of the joint chiefs had visited Israel for over a decade.

Israeli Defense Minister Ehud Barak has visited Washington four times so far this year, a schedule unmatched by any recent Israeli defense minister.

"There's been a constant stream of American officers coming through," said one senior Israeli army officer. "I haven't seen anything like it in my 20 years in the army."

Write to Charles Levinson at charles.levinson@wsj.com