The provisions of the Jones Act have been controversial for a long time. For example, one dispute arose concerning who qualified as a "seaman" for the purposes of applying the Jones Act protections. In one recent case, Chandris Inc., v. Latsis, the US Supreme Court ruled that anyone who spends more than 30% of his or her time working on a vessel sailing on navigable waters qualifies as a seaman under the Jones Act. This decision provided a quantifiable way to determine eligibility for Jones Act protection, and was issued in the vein of other decisions which determined seaman status based on an individual's exposure to the "perils of the sea."



Another controversy surrounding the Jones Act revolves around its economic impact. Opponents of the Jones Act argue that it unnaturally raises the cost of operating ports in the United States. They also contend that, because of Jones Act restrictions, shipping companies are more likely to maintain old US-built ships than to buy new ones, and that the US shipbuilding industry has suffered as a result. A study conducted by the US Department of Commerce showed that US shipyards only produced 1% of the world's large commercial vessels. Opponents of the Jones Act argue that it has resulted in an inordinately high price tag for American-built vessels. This exceptionally high price tag has prevented American-built ships from being as common on the seas as they once were.

On the other side of the debate, people who are in favor of the Merchant Marine Act point to the effects that it has had on the working environments for sea workers. The often dismal conditions endured by workers who spend their time on foreign vessels, say proponents of the Jones Act, are largely avoided in the United States because of the protections extended by the Jones Act.

Despite the debate over the Jones Act, there is little doubt that it has significantly changed the United States shipping and marine industries. From the viewpoint of a sea worker, the Jones Act helps guarantee a safe working environment and provides legal protections that were unavailable under international maritime law.