Sirens sounded in the southern Israeli district of Abu Qrenat near the Dimona nuclear reactor on Thursday, the Israeli army said without immediately providing further details.
A Reuters reporter, about 90km from the site, heard the sound of an explosion minutes before the army’s text message.
Such siren warnings are usually triggered by rocket attacks.
Israel’s army radio said that if such an attack were to take place early Thursday, its origin was not immediately clear.
Abu Qrenat is deeper within Israeli territory than the usual series of Palestinian militant rockets in the Gaza Strip.
Israeli media have been saying for weeks that air defenses in the vicinity of Dimona and the Red Sea port of Eilat are intensifying in anticipation of a possible long-range missile or drone attack by Iranian-backed forces – perhaps as far away as Yemen.
Tensions are high between Israel and Iran over Tehran’s nuclear program and a recent surge in sabotage attacks, some of which blame arch-enemies.
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