The army 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).
"The explosive sounds heard in the last few minutes are from the interceptors. The result of the interception is under review."
Yemen's Huthi rebels have been launching attacks against Israel and its interests in what they say is solidarity with Palestinians during the ongoing war between Israel and Hamas in the Gaza Strip.
The rebels belong to Iran's so-called "axis of resistance", which includes Tehran-backed militant groups in Iraq, Syria and Lebanon.
Since November, the Huthis have launched a flurry of missile and drone strikes on Israel-linked shipping in the Gulf of Aden and the Red Sea.
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, with a rebel official vowing at the time to "meet escalation with escalation".
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