"An examination by the IAF (Israel air force) and the Home Front Command found that the missile fired from Yemen toward Israeli territory was successfully intercepted," the army said in a statement.
The military had previously said it made "several attempts" to shoot down the missile, adding it had "likely" succeeded.
It later reported that shrapnel from the missile "fell inside a civilian house" in the community of Mevo Beitar, near Jerusalem, and that additional shrapnel was found in the nearby town of Tzur Hadassah.
Tuesday's attack came less than a day after Yemen's Huthi rebels said they had launched a missile towards the commercial hub of Tel Aviv, which Israeli forces said was intercepted "prior to crossing into Israeli territory".
The Huthis also claimed the Tuesday morning attack, saying they had launched a "hypersonic ballistic missile" at "occupied Jaffa", a reference to Tel Aviv.
Later on Tuesday the rebels claimed to have launched two attacks on Israel. The Israeli military did not issue any alerts or report intercepting any projectiles.
There were no sirens in either city and the Israeli military did not mention any incidents.
The Iran-backed rebels have pledged to continue their attacks until "the end of the aggression against the Palestinians".
Since the war in Gaza broke out in October 2023, the Huthis have repeatedly fired missiles and drones at Israel in what they say is a show of solidarity with the Palestinians.
The rebel group controls swathes of Yemen, and Israel has struck Huthi targets several times inside the country including in the capital Sanaa.
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