A federal appeals court in New York ordered the state to rewrite the regulations in an apparent victory for green groups who viewed them as too soft.
The 2nd US Circuit Court of Appeals said the Environmental Protection Agency (EPA) acted "arbitrarily and capriciously" by following international standards in 2013, Reuters reported.
This was despite technology being available to toughen the rules up, it added.
Circuit judge Denny Chin also said the EPA, using its authority under the Clean Water Act, should have considered onshore facilities to treat ballast water rather than focus on pollution controls aboard ships, where a lack of space might limit their effectiveness.
The US Department of Justice is reviewing the decision.
