Residents told local media that they heard two explosions after rushing to shelter houses on hearing warning sirens.
Police said there are no reports of casualties or damages so far.
The city's mayor, Meir Yitzhak Halevy, told Army Radio that the rockets, apparently fired from Egypt's Sinai Peninsula, struck open areas.
Army Radio also reported that two rockets hit the neighbouring Jordanian city of Aqaba, which was promptly denied by Jordanian authorities.
The anti-missile Iron Dome system deployed outside the city located the incoming rockets but was not activated, the army said.
Israel has increased security along the Egyptian border and is constructing a barrier to stop militants and illegal migrants from crossing over.