SEOUL—The South Korean government is investigating the whereabouts of thousands of tons of suspected North Korean coal that entered its ports last year despite a ban on such shipments, in what would be another example of Pyongyang exploiting gaps in the U.S.-led sanctions regime.

About 9,000 tons of North Korean coal, worth at least $325,000, appear to have been shipped to South Korea in October after having been unloaded and reloaded in the port of Kholmsk, on the Russian island of Sakhalin, in an apparent attempt to obscure...