Sirens sounded in the southern Israeli district of Abu Qrenat near the Dimona nuclear reactor on Thursday, the Israeli military said without immediately providing further details.
A Reuters reporter about 90 km away from the site heard the sound of an explosion minutes before the military's text message.
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Such siren alerts are generally activated by rocket attacks.
Israel's Army Radio said that, if such an attack had taken place early on Thursday, its origin was not immediately clear.
Abu Qrenat is deeper within Israeli territory than the usual range of the rockets of Palestinian militants in the Gaza Strip.
Israeli media have said for weeks that air defences in the area of Dimona and the Red Sea port Eilat were being beefed up in anticipation of a possible long-range missile or drone attack by Iranian-backed forces – perhaps from as far away as Yemen.
Tensions are high between Israel and Iran over Tehran's nuclear programme and a recent surge in sabotage attacks, some of which the arch-foes have blamed on each other.
