The South Korean ferry was carrying 459 people when it sank in the Yellow Sea.
One jet made "numerous close-range” passes near the USS Donald Cook, the Pentagon said.
The visit comes as he tries to settle ongoing tensions between China and Japan.
Five Democratic senators are pushing for the ban.
Defense Secretary Chuck Hagel on Monday said that he is backing the Navy as it considers banning the sales of tobacco products on all ships and bases.
Navy leaders say they support the Pentagon’s push for a new round of base closures in 2017 — but that the Navy doesn’t need its bases cut.
A sailor reportedly was shot and security killed a civilian.
The Pentagon has said that the deadly 2011 helicopter crash was not compromised.
A Pentagon review found "missed opportunities."
A SEAL team took control of the tanker in waters near Cyprus.