One bus was traveling from Beersheba to Eilat when three militants armed with Kalashnikovs opened fire about 30 kilometers north of Eilat near Netafim, causing multiple injuries, Israeli channel 10 reported.
Reports suggest that armed men opened fire from a car following the bus.
An Israeli army statement said that five soldiers were among a total of nine people injured.
"This morning’s incident, near the southern Israeli city of Netafim, left four soldiers moderately injured and one soldier lightly injured."
"Several people were injured as a result of an explosive device, detonated on an IDF force that arrived at the scene and drove over it," a statement said.
A second bus and a car were reportedly attacked soon after with a correspondent from Al-Arabiya reporting that five people had been killed, with one killed in the first bus attack.
Israeli media reports say that at least five people were killed in all attacks.
In a third incident, mortars were reportedly fired at Israeli forces near the southern border causing injuries, although initial reports are unsure as to the origin of the artillery.
Israeli media reported that Jordan warned Israel about an unknown group crossing its border before the attack took place.
Meanwhile, Israel defense minister Ehud Barak has said that "this terror attack originated from Gaza. We will exhaust all measures against the terrorists," Ynet reported.
An Egyptian official said that "Egypt was in no way involved in the incident, since it is difficult to penetrate the Egypt-Israel border," the Israeli daily noted.
Security forces are still investigating the nature of the incidents and latest reports from Israeli radio suggest three of the attackers have been killed by Israeli forces, with the clashes now over.
A search is currently underway in Eilat to locate other suspects in the attack, as the police presence across Israel intensifies.
Twenty five people have been taken to Eilat hospital, Arabic media reported, and emergency services were immediately deployed to the scene of the attacks.
The identity of the attackers is unknown.
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