"A missile that was launched from Yemen and crossed into Israeli territory was intercepted," the military said in a statement posted to its Telegram channel.
"A report was received regarding shrapnel from the interception that fell in the area of Modi'in in central Israel. The details are under review."
Israel's emergency service provider, Magen David Adom, reported that it had treated several people who were injured or experienced panic attacks on their way to shelters after air raid sirens sounded in the centre and south of the country.
Hours later the military announced that it had also shot down a drone launched from Yemen.
The drone was intercepted before it entered Israel, the military added.
On Tuesday, Israel also said it had intercepted a missile launched from Yemen.
Much of Yemen is controlled by Iran-backed Huthi rebels, who have been firing missiles and drones at Israel -- as well as at ships in the Red Sea and Gulf of Aden -- in what they say is solidarity with Palestinians during the Israel-Hamas war in Gaza.
The Huthis have stepped up their attacks since November's ceasefire between Israel and Iran-backed Hezbollah in Lebanon.
Israel has also struck Yemen, including targeting Sanaa's international airport at the end of December.
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