Sirens sounded after a projectile was launched in Yemen, the IDF said early on Tuesday hours after a missile launched by the Houthi rebels was intercepted.
The military said several attempts were made to intercept the missile adding it was likely intercepted.
The Ben Gurion International airport resumed takeoffs and landings after it suspended operations for a short while and El Al flights from Zurich and Larnaca were made to turn away from the Israeli coast and wait for further word before being allowed to land.
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At least 11 people were injured as they rushed for shelter, emergency service Magen David Adom said.
Shrapnel from the intercept fell in the greater Jerusalem area causing some damage but no injuries.
The Houthis announced they had fired a hypersonic ballistic missile at the Israeli Defense Ministry in Tel Aviv which reached its destination. The missile strike was the third Houthi attack on Israel in a 12-hour period after a drone was launched in the morning hours on Monday and a missile in the early evening.
"The attacks will continue until the fighting in Gaza ends and the siege on the enclave is lifted," a Houthis spokesperson said.