“The enemies of the Iranian nation should understand that any violation of our airspace will cause them significant harm,” the military head said.
The missiles were launched only three hours apart, and sirens were only activated in the West Bank.
Houthi military spokesperson Yahya Saree said the group was responsible for Sunday's attack, adding that it fired a missile toward the Ben-Gurion Airport.
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Magen David Adom said that there were no reports of injuries, except for a single case of a man who was injured on the way to a protected area.
Saturday night's sirens came after the IDF struck two Houthi-controlled ports in Yemen that were used to transfer weapons.
The warning was sent at 9:45 a.m. on Wednesday, following a similar warning against the Houthis on Sunday, in which the IDF also did not actually attack.
The last sirens that were sounded in the Israeli capital occurred 13 hours prior, also due to a missile launch from Yemen, and the third missile that fired towards Israel in two days.
Following the sirens, the IDF announced that the missile had been intercepted.
This follows President Donald Trump's Tuesday announcement that the US would stop bombing the Iran-aligned Houthis in Yemen, saying that the group had agreed to stop attacking US ships.