Yemen, at the forefront of Western security concerns since a failed December attack on a US-bound plane, boosted security on its coast earlier this year to prevent fighters reaching its shores from nearby Somalia to reinforce al-Qaeda in Yemen.
Al-Qaeda's Yemen-based arm claimed responsibility for the failed December plane attempt.
Western allies and neighbouring oil exporter Saudi Arabia fear al-Qaeda is exploiting instability on several fronts in impoverished Yemen to recruit and train fighters for attacks in the region and beyond.
The transportation department statement said more sophisticated methods of attack by al-Qaeda in the waters near Yemen could include missiles or projectiles.
"All vessels transiting the waters in the vicinity of Yemen are urged to operate at a heightened state of readiness," the statement said, adding that vessels were at greater risk in areas of limited manoeuvrability or while anchored or at port.
The US navy warship USS Cole was hit by a suicide attack in the Yemeni port of Aden in 2000 leaving 17 navy personnel dead and 39 wounded. Al-Qaeda claimed responsibility for the attack.
Two years later an al-Qaeda attack damaged the French supertanker Limburg in the Gulf of Aden.