The attack was carried on Wednesday morning, causing explosions in the area, with no immediate reports of damage or casualties.
"There were two rockets fired from Sinai, both landed in open spaces" near Eilat, an Israeli military spokeswoman said.
Egypt, however, denied reports that the rockets had been fired from Sinai Peninsula.
"We have not been informed of any violations along the Egyptian border," said an Egyptian security official, who spoke on the condition of anonymity.
"Sinai is under Egyptian security control mainly in the border areas with Israel and the Gaza Strip," the official added.
Sirens went off just before the twin blasts occurred. The city’s airport was closed and police ordered residents to stay indoors.
Security sources said that Israel’s Iron Dome missile batteries, which were deployed outside Eilat last month, did not intercept the rockets. The batteries may have malfunctioned or were not able to lock onto the rockets.
In April 2012, a rocket fired from Sinai hit Eilat, while another unexploded rocket was found near the city days later. The incident caused no casualties.
In August 2012, two other rockets also hit the city, with no injuries again.