Jodanian Information Minister Nabil al-Sharif said initial investigations indicate the rocket was a Russian-designed Grad that was fired from beyond Jordan's borders. He said authorities continue to look into the explosion to determine exactly where the missile was launched from.
Al-Sharif, who is also a government spokesman, told The Associated Press the rocket damaged a refrigerated warehouse on Aqaba's northern outskirts. No deaths or injuries were reported.
Earlier Thursday, police said they found the remains of what they thought was a Katyusha rocket. They said they were trying to determine the launch site and who might have been behind the attack.
Aqaba residents reported hearing at least two early morning explosions in the city.
Israeli media also reported that two rockets hit Aqaba and Israel's nearby port of Eilat.
The Israeli army said it searched the Eilat area after the reports surfaced but found no evidence of anything landing in Israel.
The incident occurred as jitters were high a week after Israel issued an "urgent" warning to its citizens to leave Egypt's nearby Sinai Peninsula immediately, citing "concrete evidence of an expected terrorist attempt to kidnap Israelis in Sinai."
An Egyptian security official, who also spoke on condition of anonymity because he wasn't authorized to release information to the media, denied reports that rockets were fired from Sinai on Thursday.
The damaged warehouse was at an industrial complex at the entrance of Aqaba, 210 miles (350 kilometers) south of the Jordanian capital, Amman.
In 2005, al-Qaida terrorists used the area to fire Katyusha rockets at a U.S. warship docked in the port there.
The rockets missed the ship but hit a Jordanian army warehouse, killing a Jordanian soldier. Eight al-Qaida terrorists were arrested and later received prison terms ranging from seven years to death sentences.
Israel's anti-terror office issued the warning last week and maintains a standing travel advisory telling Israelis to stay out of the Sinai desert because of the threat of terror attacks.
The Grad, known as the BM-21 Grad, is a truck-mounted 122-mm multiple rocket launcher developed in the early 1960s in the Soviet Union. Military experts say it's maximum range is 25 miles (40 kilometers).