"Following the sirens that sounded a short while ago in a number of areas in Israel, a missile launched from Yemen was intercepted by the IAF (air force) prior to crossing into Israeli territory," the military said in a statement.
AFP journalists in Jerusalem had reported air raid sirens wailing in the city.
In a statement on Telegram, Yemen's Iran-backed Huthi rebels claimed responsibility.
"The Yemeni Armed Forces' missile force carried out a qualitative military operation targeting an Israeli military target south of the occupied Jaffa region with a Palestine 2 hypersonic ballistic missile," the statement said.
The Houthis had threatened to escalate attacks in support of Palestinians following Israel's renewed attacks on the Gaza Strip this week.
"These operations, in addition to the ban on Israeli navigation, will continue until the aggression on Gaza stops and the siege is lifted," the latest statement said.
On Thursday, Israel's military said it intercepted a projectile fired from Gaza while two others fell in an uninhabited area after sirens sounded in central Israel.
Hamas's armed wing said it had fired rockets at Israel's commercial hub of Tel Aviv in response to what it called "massacres against civilians" in Gaza.
Earlier Thursday, the Israeli military said it had intercepted a missile launched from Yemen, which the Huthi rebels claimed was a "hypersonic ballistic missile" that had targeted Israel's main international airport.
The Huthis in a statement also said they had again targeted an US aircraft carrier group in the Red Sea, the latest attack after a series of intense American strikes against the Yemeni rebels.
The Huthis had targeted ships in the Red Sea and the Gulf of Aden after the start of the Gaza war on October 7, 2023, claiming solidarity with Palestinians.
They had paused their attacks for the duration of an Israel-Hamas ceasefire that began mid-January, but resumed launching missiles and drones after the United States carried out deadly strikes on Yemen Saturday.
Israel resumed its air campaign in Gaza early Tuesday with a wave of deadly strikes, shattering a relative calm that had pervaded in the war-ravaged Palestinian territory since the ceasefire took hold.
The territory's civil defence agency said Thursday that 504 people had been killed so far in the renewed Israeli assault, including more than 190 children.
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