Aljazeera correspondent Yasser Abu Hilala quoting witnesses said the rockets were fired on terminal seven. This particular terminal is usually reserved for military vessels.
The rockets fell near a US Navy vessel, anchored on the port for almost a week.
The authorities have closed the entire area and begun combing it to identify the site from where the rockets were fired.
There was no immediate report of damage.
Aqaba is located next to the Israeli resort of Eilat and is strategically important to Jordan as it is its only seaport.
Eilat incidentIsraeli public radio also reported that a rocket had exploded in Eilat, although it was not clear if it was the same incident.
Earlier, Jordan's Interior Minister Awni Yarfas said, "They (the authorities) heard a strong blast, its source is unknown and security forces are investigating the source of the explosion."
Blasts were heard at about 9am local time (0600GMT) near Aqaba, a Red Sea port 350km south of the capital Amman. according to an official at the Aqaba Port Authority.
Two US military vessels have been docked in the port for the past 10 days, witnesses said.
Jordan tightened security after
Sharm al-Shaikh blasts
US officials could not immediately be reached for comment.
In October 2000, 17 US sailors were killed when two bombers on an inflatable raft blew themselves up alongside the USS Cole, a destroyer, in Yemen's southern port of Aden.
Jordan itself boosted security at tourist resorts and in
populated areas in the wake of the deadly bombings in the Egyptian Red Sea resort of Sharm al-Shaikh last month.
Earlier this month, Israel warned its citizens to steer clear of
neighbouring Jordan, saying there had been an increase in the threat of attacks against travellers and tourist sites.
Jordan, one of the most stable countries in the Middle East, is
one of only three Arab states to have diplomatic relations with
Israel but, unlike the Red Sea resorts of Egypt, it is not a regular destination for Israelis.