While publicly pressuring Israel to make deeper concessions to the Palestinians, President Obama has secretly authorized significant new aid to the Israeli military that includes the sale of 55 deep-penetrating bombs known as bunker busters, Newsweek has learned.

In an exclusive story to be published Monday on growing military cooperation between the two allies, U.S. and Israeli officials tell Newsweek that the GBU-28 Hard Target Penetrators—potentially useful in any future military strike against Iranian nuclear sites—were delivered to Israel in 2009, just several months after Obama took office.

The military sale was arranged behind the scenes as Obama’s demands for Israel to stop building settlements in disputed territories were fraying political relations between the two countries in public.

The Israelis first requested the bunker busters in 2005, only to be rebuffed by the Bush administration. At the time, the Pentagon had frozen almost all U.S.-Israeli joint defense projects out of concern that Israel was transferring advanced military technology to China.

In 2007, Bush informed Ehud Olmert, then prime minister, that he would order the bunker busters for delivery in 2009 or 2010. The Israelis wanted them in 2007. Obama finally released the weapons in 2009, according to officials familiar with the still-secret decision.

James Cartwright, the Marine Corps general who served until August as the vice chairman of the Joint Chiefs of Staff, told Newsweek the military chiefs had no objections to the sale. Rather, Cartwright said, there was a concern about “how the Iranians would perceive it,” and “how the Israelis might perceive it.” In other words, would the sale be seen as a green light for Israel to attack Iran’s secret nuclear sites one day?

“If we say yes, have we somehow given someone a green light without intending to? Whether that green light was an Israeli green light to go do something or whether it was a message to the Iranians, OK these guys aren’t serious about talking, they are starting to arm themselves,” Cartwright explains.

U.S. and Israeli officials told Newsweek that Israel had developed its own bunker-buster technology between 2005 and 2009, but the purchase from the U.S. was cheaper.

Uzi Rubin, the first director of the Israel Missile Defense Organization, between 1991 and 1999, and currently a military technology consultant to Israel’s Ministry of Defense, says U.S. officials originally had concerns about “how you use the bomb, where you use the bomb. These could be used in civilian areas because Hamas and Hezbollah intentionally bury their rockets in villages and towns,” he explained.

Obama’s security cooperation extended beyond bunker busters. According to Rep. Steve Rothman (D-NJ), who serves on the committees that fund both the U.S. military and foreign aid, Obama gave “orders to the military to ratchet up the cooperation at every level with Israel.”

While the Obama administration has touted some public cooperation with the Israeli military, Newsweek’s article Monday will reveal other covert efforts by the U.S. military to aid Israel in the volatile Middle East region, and the impact the improving military cooperation has had on the sometimes chilly relations between Obama and Prime Minister Benjamin Netanyahu, and the president’s popularity in the American Jewish community.