Israeli officials have been lobbying Washington to reverse its decision which was put in place after a Hamas rocket struck close to the airport on Tuesday. Other international airlines followed suit, canceling many flights to Israel's Ben Gurion International Airport in the last two days.
Now that the ban is lifted, the three U.S. airlines that fly to Israel -- Delta, United and US Airways -- will need to decide when they will resume flights.
In a statement released late Wednesday evening, the FAA said it "worked with its U.S. Government counterparts to assess the security situation in Israel and carefully reviewed both significant new information and measures the government of Israel is taking to mitigate potential risks to civil aviation."
The Obama administration came under some criticism by a key pro-Israel lobbying group, and also Texas Republican Senator Ted Cruz who had alleged the ban was put in place to pressure Israel to agree to a cease fire.
The charge was denied by US officials, including Deputy National Security Advisor Anthony Blinken who insisted to CNN's Wolf Blitzer that politics played no role in the decision.
"We didn't use the FAA to do anything. The FAA makes independent judgments for safety and security of our airline passengers and for our airlines," Blinken said. "They made a judgment and we're not in the business of second guessing the FAA or overturning what they do."
Former New York Mayor Michael Bloomberg flew to Israel on El Al airlines as a show of support for Israel. Speaking to Blitzer, Bloomberg said he thought the FAA made a "mistake."
"We certainly don't want to stop flights into airports in America," he said. "It would be devastating for America. It's devastating for Israel when you stop flights."
The FAA said it is continuing to monitor the "very fluid situation around Ben Gurion Airport and will take additional actions, as necessary."
(Adam Levine, CNN - CNN's Rene Marsh and Mike Ahlers contributed to this report)
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