It said in a statement that "a surface-to-surface missile was identified crossing into central Israel from the East and fell in an open area. No injuries were reported."
"The missile was fired from Yemen," it added in a subsequent statement sent just before 7:00 am (0400 GMT).
It said explosions "heard in the last few minutes" were from air-defence interceptors.
"The result of the interception is under review," the military said.
Yemen's Iran-backed Huthi rebels have been launching attacks against Israel and its perceived interests in what they say is solidarity with Palestinians during the ongoing war between Israel and Hamas in the Gaza Strip.
The rebels are part of the "axis of resistance", which also includes Tehran-aligned militant groups in Iraq, Syria and Lebanon.
Since November, the Huthis have launched regular missile and drone strikes on what they deem to be Israel-linked shipping in the Gulf of Aden and the Red Sea, waterways vital to global trade.
And in July, they carried out a drone attack on Tel Aviv that killed an Israeli civilian.
Israeli warplanes bombed the Huthi-controlled Yemeni port of Hodeida in response, destroying much of the facility's fuel storage capacity and killing several people, according to the rebels.
A rebel official vowed at the time to "meet escalation with escalation".
A Huthi statement last month affirmed "once again that the Yemeni response is definitely coming".
Regional hostilities
Since Hamas's October 7 attack on southern Israel, which triggered the war in Gaza, hostilities with Iran-backed groups around the Middle East have flared.
The Lebanon-based Hezbollah movement, in particular, has been trading regular cross-border fire with Israeli forces that threatens to spiral into all-out war.
The hostilities have displaced thousands of people in both countries from their homes near the border
Hezbollah number two Naim Qassem warned in a speech Saturday that "if Israel does unleash a war, we will face up to it -- and there will be large losses on both sides."
"If they think such a war would allow the 100,000 displaced people to return home... we issue this warning: prepare to deal with hundreds of thousands more displaced."
The cross-border violence since early October has killed 623 people in Lebanon, mostly fighters but also including at least 142 civilians, according to an AFP tally.
On the Israeli side, including in the annexed Golan Heights, authorities have announced the deaths of at least 24 soldiers and 26 civilians.
Hezbollah has said it is acting in support of its ally Hamas in the Gaza Strip.
The war in Gaza broke out after Hamas attacked Israel on October 7 resulting in the deaths of 1,205 people, mostly civilians, according to an AFP tally based on Israeli official figures.
Militants also seized 251 captives during the attack, 97 of whom are still held in Gaza, including 33 the Israeli military says are dead.
Israel's retaliatory military campaign has killed at least 41,182 people in Gaza, according to the Hamas-run territory's health ministry, which does not provide breakdowns of civilian and militant deaths.
